So, a fairly standard encounter is that the players will go to a shop to replenish some supplies. They will try to haggle for a better price, but a decent amount of the time they will not succeed (usually by a failed Persuasion check). If the party has even an ounce of "murder-hobo" tendencies, then they will in many cases try to threaten or attack the shopkeep for a better price, or even straight up steal what they want. 

I was wondering what techniques different people have used for protecting the shopkeep. Do you favor trying to dissuade players from threatening in the first place or do you favor letting the players do what they want with the helpless fellow and then punish them after the fact?  

I have heard of some DMs making the shopkeep secretly be a high level ex-adventurer, but after one or two encounters like that the strategy will begin to feel unnatural or overused. 

Ive had a few ideas myself but wanted to hear what other people like to do

• Does the shopkeep have some sort of (silent) alarm to alert the towns guard?
• Does the shopkeep have a hidden wall of force separating the counter from the rest of the shop? 
• Does the shopkeep maintain a small collection of counterfeit coins to use in case he is robbed and keep the money in a separate vault? 

The friendly shopkeep is one of the most integral parts of an adventuring RPG and must be kept safe at all costs

It would depend on the shop. Maybe an armory, with expensive armor, place tracking spells on items. After the party leaves, that's when the assassins are sent.

Or the shopkeepers invest in a magic item requiring a save vs wisdom at a DC to initiate violence. 

If you want more mundane strategies, guards are always nice. If they kill the guards, of course the city will get involved. I suggest the bounty go up every time they kill some. And don't be afraid to justify this. Speak with dead spells removes a lot of ambiguity.

Good shopkeeps have invested in having a wizard place very high level glyph of warding explosive runes in the shop. Shopkeeper hits their panic button and hooligans are about to get extra-crispy.

Also there's always the good old loaded-crossbow-under-the-counter trick.

In a world of magic a cleric can cast a divination spell to find out who killed the town’s favorite shopkeeper. At that point the mob will form with pitchforks and torches and they’ll be backed up by the town guard. If the party kills them ... well the king will be mightily displeased and so will his retainers...

Shops don't exist in a vacuum. Every shop fits somewhere into a network of social, economic, political, and possibly unsavory relationships. 

So, if the shop is attacked or threatened, someone from any one of those other pieces of the puzzle could seek to make it right. So let's look at each one in turn...

Social: the shop is important to the town. If word gets out that one shop is an easy target for thieves, then everybody in town could be at risk of a sudden influx of opportunistic thieves. So the people of the town will defend each other. They'll set up a neighborhood watch. Suspects and perpetrators will find themselves cut off from the goods and services of all the other shops in town. Plus.... Mob Justice can cruel and effective. 

Economic: the shop is a member of a guild. Whether a specific craft guild, like the Gemcutter's Guild or the Blacksmithing Guild, or just a sort of general Chamber of Commerce. Anyone who causes trouble at this shop could find themselves blacklisted from not just other shops in this town, but at similar shops in many other nearby towns as well. And guilds will have their own enforcers. Again - mob justice. 

Political: this is where the standard Town Guard response comes in. Roughing up a shopkeeper is easy. Roughing up 35 town guards with armor and weapons and horses and guard dogs and magic and healers and legal authority is quite another. Good luck. 

Unsavory: this is the fun one! Sometimes a shop is more than just a shop. Sometimes a shop is a front for a sinister shadowy organization that uses the shop to launder it's ill-gotten gains and to gather and spread local rumors. Maybe the shop is a front for the local thieves guild. You rough up a random shopkeeper for a discount and two nights later your horses are murdered while you're taking a long rest. Three nights after that someone slips a mickey in your drinks at a bar and you're all sickened for a few days. A week later your paladin gets a letter from their temple asking about this woman who just arrived carrying a baby and she 's claiming that the paladin is the baby's deadbeat father. Now the paladin has to go back and explain or face an atonement quest. Every town the party goes to they can't find a room at any inn or hotel because the innkeepers know better than to piss off the people who control the liquor trade. Every day the party wakes up to find that another piece of their equipment is missing - it turns out that the thieves guild is paying a bounty for gear stolen from the party. In every tavern where the party stops for lunch or dinner, the cook spits in their food.... or worse! use your imagination. 

Have fun. 

In established settlements I have two sorts of shops.  The first is a shop the adventurers would want to visit.  The second only contains mundane items the townsfolk would want.  The adventurers would only visit that shop to buy a blanket or a medium sack or something mundane like that.  But I have created a lore for the first sort of shop in my own campaigns.  I wrote quite a post about it in stories and lore about six months ago.  I'll dig up a link.  Essentially it works like this.  Shops that sell weapons, armor, potions and things of that nature are dealing in "controlled substances" that are significant to the authorities.  The Mayor doesn't want a party rolling into town, stealing a stack of weapons and ammunition and then having their way with the populace.  But such shops in the fantasy world are necessary so they exist here and there.

A shopkeeper that wishes to open a shop of this sort must obtain a charter or other authorization from the government.  With the charter, the shopkeeper gets assistance from the government.  The new shop is built ... like a bank vault.  There are a few common features to these shops.  First it is built upon a basement that is completely made of stone.  There is one way into the basement only, and that heavy door is locked by secret locks and a pressure plate.  The really good stuff is in the basement.  If the party wants to buy a weapon they must describe it to the shopkeeper and he goes into the basement and brings one back to show them.  They agree to buy it or they don't.  If not, he takes it back.  Within the basement there is a mirror that acts like a periscope where the shopkeeper can see what is going on in most of the shop while he is down there.  He has the ability to raise the alarm from within if necessary.  Guards will come.

The first floor is also made of stone.  There are no windows on the first floor and only one door.  This is a heavy door that can be locked at night to prevent entry.  But also, it must be unlocked from within to get out.  Again the lock mechanism is complicated.  Inside the shopkeeper has a table near the door for the party to sit and wait while the shopping is going on.  There are racks of goods along the wall at the front and bins and things a little further in.  In the back of the shop are a number of heavy locked wooden chests.  If the customers ask for some thing that would be in the chests, the shopkeeper invites them to sit down and he brings it to them.

There is a stair to the second level, which is mostly a balcony.  There are small windows on the second level for light to get in.  There is another stair to a third level where the shopkeeper's family lives.

The guards keep an eye out for the shopkeeper and know when someone enters the shop.  If there are any unusual sounds or events they would go in to investigate.  Also they check the signal flag outside.  There are two flags.  One shows "customer(s) inside" and another is the alarm flag.  If the alarm flag is raised, guards come.  If the customer flag is raised for a long period of time, guards come.

If there is a robbery by the party they will almost certainly be killed for it, soon, unless for some reason I wish to weave that into the story.  I don't consider the game fun if others steal what they want from law abiding folk so I am content to end the game.

***

I checked and my earlier post was not so extensive.  I developed the idea and shared it with my son.  That is why I still had those details on my mind.

When my players had their last layover in Waterdeep a gew months  ago, they stopped by Friendly Harry's shop, the magical door wouldn't open  because they needed to be "buzzed" in. Harry is a wizard/craftsman who makes his living in dealing or crafting secialty magic items (turnaround could be a few days). Harry's Iron Golem is the one who opens the door and keeps watch  over the store.  Harry doesn't personally make all the commissions he sells, but instead his team of a dozen mid level gnome wizards in the workshop behind the desk do all the real work. So between the Iron Golem, high level wizard Harry, and his dozen potent wizards, the likelihood of any sheningans  would surely be quashed.

But honestly, although it breaks the immersion momentarily to just take a pause OOC to say "hey, trying to steal from or hurt/kill a lowly shopkeeper is not very helpful for anyone, moving forward shopkeepers, children, elderly, etc. is off limits; i wont even allow an attack roll to be made" to immediately reset expectations and get the shipping back on track. Remind them they are adventurers, and such behavior really just makes them look like lowlife thugs and it hurts your personal fun from the DM side.

The shopkeeper's high-level paladin son is visiting with his adventuring party, and when they hear the sounds of distress from the shop, they charge in to the rescue...

The shopkeeper has a magic item that summons defending hellhounds. Or has a pet killer chihuahua with a billion hitpoints.

Another party of murder-hobo adventurers enters the shop, sees what's happening, and yells, "Hey. they're trying to steal the loot before WE get it!!" and attacks the party. (After driving the party off, they kill the shopkeeper and steal everything so there is no longer a shop for the party to go to.)

The shopkeeper was the owner of a chain of stores all across the country...they are all closed in mourning after the party kills the owner, and then the owner's sons get in a huge legal squabble over who inherits the business, and there is no way to buy anything anywhere for the rest of the campaign.

The owner has sold his soul to a demon lord in exchange for a long, long life, and the demon lord shows up to keep his end of the bargain.

The shop is a front for black-market trading and the local crime syndicate shows up to protect their turf.

The shopkeeper's god hears his prayer for deliverance and smites the party with lightning bolts and humiliating curses.

Depends on the shop.

Magic item shops are usually rare. And so the owner is at least powerful in some area. The very (very) high level wizard with his magic item shop I have for new players has glyphs of warding on his cases. With 8th lvl blights. That is what I tell the players if they ask me out of game or make an arcana check. It is used simply to show them that not everyone is to be ****ed with. They have to pick their fights if they want to be murder hobos.

Normal shops. Now that is a different story. A smith maybe has a level of fighter or two. But not all. But shops like smiths, or general stores have mundane means of protecting their shop. So they are easily robbed by a level 2 sorcerer. But still, they gotta get away with it. I don't always protect my shop keepers. Only if it makes sense. As if the players want to rob it perhaps kill the owner, damn right they can do that (unless reason happen). I like to give newer players the option to feel the freedom of D&D. And if that freedom is killing my shop keepers then they gotta find a shop keeper to kill. But, it is still very hard to murderer someone and get away with it. Because if the town has money, it would probably hire an investigator. And many of them have divination magic. So what happens if a Speak with dead is suddenly cast on the subject. Or a Raise Dead?