Building my first campaign world, I've only run premade oneshots so far, and I'm curious how others determine what's a reasonable number of high CR monsters for their campaigns? By reasonable I mean feels good, has a good amount of tension or threat but doesn't make the players wonder why the monsters just haven't taken over already.

Quick context - I'm thinking my campaign will take place in a small to mid sized nation (I'm reskinning Amn in Toril) that's broken off from a larger empire maybe 150ish years earlier. I like the idea of having two dragons (one more aggressive, and one more open to negotiation), a small incursion of Giants, some sort of kraken or underwater type cult, and maybe a demon / devil type encounter taking place sometime throughout the campaign. 

That being said, I know things will change as the players go through the campaign and I'm trying not to over plan everything from the start. So how do you figure out this balance?

I run a game that does not have MMORPG-like zones.  Dangerous things of all sorts (low to high CR threats) can be found anywhere.  I do not expressly make those threatening monsters attack the party, but they can find traces of them routinely as they travel.  My last group found a steaming pile of dragon feces next to an empty horse paddock.  That "encounter" arose from a random monster chart indicating a dragon.

https://www.worldanvil.com/w/land-of-the-fallen-7Blandfall7D-masterwitch

As a world builder I am obsessed with demographics. I found that a combination of CR and plans give a pretty clear population. The above link is my world but if you look under little woods law you will find my demographic information that includes PC, NPC'S, and monsters. Obviously a world like say Dragonlance will have more dragons but a basic DnD world pretty much fits my numbers.

Typically in a campaign, your party will encounter high CR monsters when they are higher level because the storyline takes them to places where those denizens are found.

Levels 1-5: The PCs are likely to be adventuring around in a remote area - there'll be a couple of villages, forests, some old mine shafts etc.

Levels 6-10: As the campaign story arc takes off and the PCs are up for more dangerous jobs, they head to more dangerous places. A city teeming with corruption, the ancient ruins where an artefact was once forged, a lost dwarven city, the mindflayer hives in the underdark.

Levels 11-15: The PCs are now renowned as great heroes through the land. When NPCs come to them seeking help, they are looking for those guys that stopped the mind flayer invasion. Now their help is needed to venture into the destroyed kingdom where a council of liches still rule, the territory claimed by the red dragonflight, and may even venture into the elemental planes or the hells to retrieve magical artefacts. Moreover, the PCs probably own castles of their own, run guilds and maybe even thrones.

Levels 16+: The PCs are almost as powerful as demi-gods. They bend and shape matter to their will with ease. They travel to other dimensions, challenge the avatars of gods, maybe even enter the Far Realm to fight Great Old Ones in their own domain.

Because the storyline challenges will change with the party level (naturally, and in line with what the PCs can handle), they will face mightier and mightier challenges as the game progresses. They may also meet vastly over-tuned creatures earlier on, but in a non-combat capacity (at level 3 they might meet the archmage who gives them their mission, or see an adult green dragon from afar).

Don't try to build a world in such detail to start with that you feel a need to list what monster exist. Let the world change and evolve in line with the story that develops between you and the PCs. By the time the party are level 11, you'll need to put them in fights against CR20 creatures pretty much every session if you want to provide decent challenges and are only running 2-3 encounters per day. So those high CR monsters will be very rare in the world, but they won't be rare to the PCs because the PCs are actively seeking them out, going to their lairs, and generally being key participants in the adventures. In the same way, I've never seen a lion in the wild, but for a safari ranger, they see them every day. 

My party is currently running through a slightly modified version of Storm King's Thunder on the Sword Coast, so it is quite a big area.

Through levels 6 - 10, once they were able to start exploring the world, they have encountered 2 creatures with a CR of at least 20 (One of whom was killed by a bunch of fire giants), 3 creatures with a CR between 15 and 19 and 12 creatures with a CR between 10 and 14 (5 of them killed). These creatures are a mix of enemies they had to flee, NPC's who may eventually turn on them and bosses of chapters and side quests.

There are 2 creatures with a CR of at least 25 they will almost certainly meet before the end of the campaign (But probably not fight), and a load of creatures with a CR between 10 and 20 who act as bosses or mid-bosses of chapters and sidequests.

Only about 1/3 of them are present in the actual adventure book for Storm King's Thunder, with the rest being added over time to make the enemies more appropriate to their skill level, the world larger and to feed my addiction of giving class levels to monsters.

You don't have to plot it out at the beginning of your campaign. Your world will have as many high CR creatures as your PCs need to face. 

The PCs may not even be aware that there are high CR monsters in the world.

Quote from Wysperra >>

You don't have to plot it out at the beginning of your campaign. Your world will have as many high CR creatures as your PCs need to face. 

The PCs may not even be aware that there are high CR monsters in the world.

 I don't even know how I'd figure it out before the campaign started. My PCs are currently level 11. I'd originally intended them to reach a certain area at a level where a trio of 2 Green Hags and a Night Hag might provide a decently challenging encounter. I just stuck an additional CR15 monster into the mix because I know they would cut those hags to pieces in a matter of moments.

The campaign has also ended up running way longer than anticipated. We intended to play to level 5 and then see, so the BBEG was a level 9 warlock. They toasted him at level 5, he came back as a remade construct version of CR11. The final campaign boss is now going to be CR25.

Challenge is relative.

A party of 1st level adventurers will be panicked to learn that there is a nearby young dragon.  A group of level 5 characters are more like "Meh, we got this" and to a level 10 party, that young dragon is a speed bump on to other fights.

From a world building view you can do one of two things:

Preplanned- Put stuff in the world and hope the PC's go where they're supposed to go for their level.

Story planned - Adjust the challenge for the PC's wherever they are, and hope that it all feels cohesive and logical later.

I tend to be more Story Centric with ramping up my difficulty for encounters at each step.  That way I know that each encounter will be a challenge for the party when they hit it.

My only other advice:  Never make the party roll dice when the outcome is all but decided.  If a group of level 7 characters come upon a kobold encampment, unless there's an actual dragon hiding in it, there is no challenge the party will wipe out the kobolds.  Generally it's better to narrate that and move on rather than rolling dice for each swing and miss/ hit.  The exception would be if the party needs/ wants a clean win and a chance to just "go to town" which sometimes they need with a real easy win just to have fun with their powers.

I think what you have described is more than fine, realistically there can be high CR monsters in your world that don't need to be apocalyptic level threats. They may have no interest in destroying humanity unless provoked to do so (think Smaug). I think having multiple threads/threats to follow is something that gives the players choice, this said I would still be careful not to overdo it where the players get overwhelmed. Unfortunately for this there is no magic number and it heavily depends on your party/group, but giving them the option of exploring different big bads I think is a very neat idea especially if you can tie them together later into a large scale threat.

General advice that I like to share is once the party is lvl 12/13 they are ready to take on most big threats that will be present in your world.