5e has a bit of a reputation for not really valuing magic items correctly... there are a few "uncommon" magic items that are more valuable and useful than rare items, and the rough values given for different magic item rarities are also a little unreliable. Some of the text in the PHB and DMG even implies that magic items of any type are extremely valuable and, among other things, you probably won't be able to casually find someone to sell magic items to who can actually properly compensate you for their value.

That said... magic shops are pretty common in D&D, usually operating more like magic shops that you see in videogames. So far I have included magic shops in my games... I try to keep the selection pretty light, with more focus on trying to include interesting common or uncommon items than anything too mechanically useful. So I'm just curious how other DM's feel about magic shops... do you leave them out entirely? If you do have them, do you try to make stuff actually affordable? Also... do you include any interesting defense systems just in case you've got a murder hobo in your party who will happily murder the shopkeep and just steal everything?

magic shop generator ia an excellent resource, google it.

It is worth mentioning that if you're too generous with magic items, you won't have anything to give to your players, as they will already have everything they want. It's still okay to make magic items common, so long as you don't do any of a certain rarity or higher outside of high-stake rewards. Common items are fine, uncommon less so, but once you hit rare the value of magic items drop significantly. Make sure you know exactly what you're putting into a shop to avoid railroading.

Yes I use them, I would argue they are borderline necessary.  Besides big ticket things like a fortress or warship, players have nothing to spend gold on later on in the game.  What I do is have certain types of shops sell certain types of magic items, on a per session rotating basis in addition to the mundane stock, to keep a certain level of believability. How I do it is: 

The Blacksmith: Buys and sells all weapons and tools in the PHB, plus has a magic weapon on rotation. 

The Armorer: Buys and sells all armor and tools in the PHB and has a magic suit of armor on rotation. 

The Jeweler: Buys and sells clothes, gems, art objects and jewelry, has either a magic ring or rod on rotation.

The Mage's Shop: Buys and sells arcane focuses and spell component plus has either a wand or staff on rotation, as well as 3 scrolls on rotation.  

The Alchemist: Buys and sells potions, having 4 on rotation 2 being healing the other 2 being specialty potions. 

The Oddities shop: Buys and sells anything on the trinket page of the PHB, or any other odd item a player describes, with a magic wondrous item on rotation.

The General Store: Buys anything at stingy prices, sells any miscellaneous items (parchment, rope, candles, foodstuffs, etc) has a 50% chance of having anything else in stock (upon a player asking) and a 1/3rd chance of having a magic item that could be anything.

What the magic item is is random, but the rarity is based on player level: 1-5 is uncommon, 6-10 rare 11-15 very rare 16-20 legendary.  Most towns have the general store, and I sprinkle 1-3 other ones depending on the towns size.

Pricing wise uncommon is 500 gp, rare is 2500, very rare is 12,000, and legendary is 45,000.  Give or take 10% based on the item in question and how I feel about it.  Cut the price in half for consumables.  The players can sell or trade for more or less full price at the respective appropriate shop, or sell a tier down at a general store.

As for some kind of robbery, the merchant obviously has magic glyphs and alarms that would blow up and summon a bunch of guards.  They are free to go for it though, I wouldn't say no you can't try.  There would be consequences obviously.

I try to find a balance between what the DMG says and what my players find enjoyable. I want my players to be able to use the wealth they've earned, but I don't want to ruin balance by having +2 swords everywhere.

In my Saltmarsh campaign I added in a magical tattoo parlor using some of the tattoos from Tasha's and some custom stuff which is flavorful from a RP perspective, but not mechanically useful. I'm also using the rules in the book for the Faithful Quartermasters of Iuz store although none of the players have attempted to use it yet. I'm probably going to include a wandering merchant that will sell some specific magical items. That way they have a way to pick something up, but won't be able to just keep coming back to buy stuff up since the merchant will have traveled away again.

I'd like to recommend the Discerning Merchant's Price Guide for pricing magic items: https://www.dmsguild.com/product/205126/Discerning-Merchants-Price-Guide

I've found it to be VERY helpful for stocking magic shops.

I do not have magic shops in my Roman Empire world.

There is a specialty place, kind of like an auction house, that deals in "antiquities" and thus magic items... but there are no magic-item wal-marts.

West coast cities like waterdeep, Neverwinter, and San Diego - yup. Most other cities-nope 

Major cities, sort of.  Permanent items are more heirlooms and property of the wealthy and powerful, if not regularly carried they are stuff kept in secured vaults and armories.  There is trade in potions and scrolls, and spell storage stuff, ensures repeat business.  Potions largely work out of storefronts.  Scrolls and spell storage items, there are certain libraries and societies one can become part of to access.  Spell tattoos are largely an underground thing.  The idea is that if the PCs ever make paydirs in coin through adventuring or downtime, these enterprises would happily relieve them of their coins, but as the players increase in power they'll sort of "outgrown" their need.  Basically some magic is common and cosmopolitan, but if that's all a PC wanted access to, they'd set up a city based career or climb the social ladder, not adventure.

My San Diego isn't very magical, but weapons and armor are much more readily available in comparison to the rest of the magical west coast cities.  

Outside of the major cities, smaller communities might have a few magical curative items and magic on hand for emergencies or given them as gifts or barter from folks passing through.  

Yes, but mine are rare (found only in a few larger towns) and have limited stock. Besides basic wizard supplies and spell components, they sell the following:

Scrolls: cantrips=25 gp, 1st level=75 gp, 2nd level=150 gp, 3rd level=300 gp.

Potions: healing=50 gp, climbing=75 gp, animal friendship, greater healing, or water breathing=100 gp.

Magic items: Bag of holding or driftglobe=400 gp. A few random common wondrous items (XGtE) for around 200 gp, and a couple uncommon wondrous items (only niche ones that will be useless in 99% of situations) for 800 gp.

For context, characters of levels 1-4 usually make about 100 gold a level in my campaigns.

Potions are acquirable in a big city.  Scrolls, it kind of depends on your connections.  If a known associate of the Thieves' Guild has an unused scroll of Dimension Door written by an underpaid adjunct professor at the university, questions will be asked.  A bag of holding; boots of elvenkind; these wouldn't be difficult to acquire with cash.

Anything anyone really wants though, I think they have to adventure for - whether that means stealing it from the guy who has it or exploring a lost city.

My game is set in Eberron, so in some sense, every shop is a magic shop. The existence of cantrips like prestidigitation means you can get (the magical equivalent of) a refrigerator or a microwave at any general store.

The more powerful items you find in the DMG are a bit different. +1 weapons are expensive but still mass-produced, but a flame tongue is probably going to be either an heirloom quest reward thing or crafted by a PC.

I want “magic shops” to impress upon my players the higher base level of technological development in the setting; the Eberron mantra of “wide, not high magic” means that the really powerful items won’t be any more common than in any other setting.

Players should not be able to pick and choose items that complement their chars perfectly. Magic items complementary to a player's abilities are force multipliers, and they quickly become a nightmare for a DM to counter. 

^^^ This.... is why I do not respond positively to players giving me "wish list" magic items. How do you even know the item is in my world? The DMG is a generic book that has generic D&D magic items... it is not a catalogue of the magic items that exist in the Roman Empire.

(Not to mention, what are you, as a player, doing thumbing through the DMG reading up on all the magic items in detail, to find the perfect one for your character? In my day that was called "cheating"... and today it would at minimum be called "spoilers.")

Nope. I do not use them, and I probably never will. If I want a player to have a magic item, I'll just give it to them. Some people deal in common magic items, but only nobles are really going to have more than one or two magic items, and they're not looking to sell them. This is also partially negated by the fact that my players don't earn very much money. They're heroes because they're good people, not because they want $$.

My setting is kind of medium-magic. Magic isn't super uncommon, but clerics don't exist, and powerful magic is extremely rare. There have only been about four level 20 characters, ever. Some of my players did start with common magic items, but I don't hand them out lightly. My party is level 5, and outside of common magic items, the Rogue has +1 studded leather and a +1 shortsword, the Sorcerer has a wand of secrets, the Bard doesn't have anything, and the Druid has a spell scroll of animal friendship.

The nice thing about being "stingy" with magic items is that even the low-end ones like a +1 dagger seem awesome and become treasured possessions, and then you don't even need the super-mega stuff like Holy Avengers before the very end of the campaign, if at all.

If you start with all the common/uncommon/rare stuff all over the place and in the shops, then you need Holy Avengers and Hands of Vecna in a treasure hoard just to make it seem like treasure.

"Magic Shops" in my worldbuilding sell blank books, paper, inks, pens, some books of magical knowledge and possibly a few things used for alchemy.  They may have some scrolls to offer once you have obtained their confidence.  The scrolls will be pretty mundane stuff.

Alchemy shops generally desire to sell finished potions.  They do not wish to sell the means of producing potions nor the ingredients.  The potions available are pretty "run-of-the-mill" stuff, but if you ask, they may have the means to brew the potion you need in three to thirty days.  Usually they will expect money up-front to brew potions on order, and some other security you will complete the transaction.

Magic items can be found for purchase only by obtaining the confidence of a merchant that "happens to have something they came across ..."  It will a specific item, or maybe two or three items, that they can sell.  They are unsure of what exactly it is, but they were "told it is a _____ or they believe it is like a ________."

The only other way to get a magic item is to work for a quest giver, obtain it in loot or murder NPCs that they know are carrying the item.

Items may be obtained from a temple, such as a scroll of cure light wounds or vials of holy water.

When dealing with "Back alley magic item purchases", you will probably need to handle that in a thieves cant type code.

Shopkeeper:  Oh, I had an unusual delivery the other day.

PC:  Really, I am always interested in unusual things.  I have developed a fondness for unusual or, even better, unique items.  I devoted a great portion of my wealth to acquiring strange things for my collection.

Shopkeeper:  Yes, yes, I understand.  It is refreshing to see something different.  I had a shipment come in and someone left their old papers in among a stack of blank paper I bought.  Shame that I didn't discover it until they had long since departed.  Now I have these old notes, of some such thing, and I don't know who to return them to.

PC:  Why if you could let me have a look, maybe I would see an identifying mark on the page that would help you return it to the owner.

Shopkeeper:  Oh that would be very nice.  But I don't know.  Let's see.  I do recall the ink was a beautiful blue ink.  Not something that I ever seen before.  Y'know I hear they use blue ink on water scrolls or elementals or something.  Such a beautiful color, that's what I remember.

PC:  Oh, I should like to see that for certain.  I've never seen blue ink.  It must be wonderful.  I tell you what (coin splat sound as he sets a pouch of coins down) I'd give you two gold pieces just to see the writing.

Shopkeeper:  Oh, well I should fetch it, but that's not all.  Why it was wrapped in a vellum sheet with some beautiful drawing on the outside.  I couldn't let you see the writing.  I'd be worried that it would fade in this bright light.  But when you see this drawing, why it is a real piece of artwork.  Now that I could let you see, but it might cost you what you have in that bag.  How much do you figure you have there?

I don't use magic shops, but I will occasionally have a magic item show up in some kind of curio. The issue of concentrated wealth aside, the rarity and price of a magic item does not necessarily reflect how powerful something is. Rarity is a function of scarcity;  how likely you are to come across something. The reasons why some items are more scarce than others are myriad and best left up to worldbuilding. But the simple answer that 5e seems to be taking is that the means of making certain items seem lost to time. That's not to say they cannot be rediscovered. But they may need to be rediscovered. What's more, you can no longer simply craft magic items by knowing or repeatedly casting certain spells. Questing for rare materials, including parts from creatures, is encouraged in Xanathar's. This makes the creation of such items more special.

I like the idea of magic items on rotation in relevant shops, rather than magic item shops.

I am working on a magic item shop myself, but it's almost entirely wondrous items with strange uses and not directly useful weapon and armour. Things like magic coins and weird potions with strange effects. There's a few weapons in the shop but I am designing the shop to be un-robbable, and it is going to be mainly the fulcrum of quest-giving rather than a place for the PCs to shop regularly, so they won't end up loaded with umpteen magical items!