After a 45 hour play through, there are a few mods I have come to realize that I either installed incorrectly (cloaks of skyrim, winter is coming, alongside CCOR) ... or wasn't interested in having such immersive jewelry...

So I un-installed and removed them from my load order.

Is it really going to cause instability in my game?

Simple answer is that when you save, data is permanently added to your save file. If the data is added by a mod and the mod is subsequently removed the inconsistency between the data in your save file and the data in your load order can cause weirdness and CTD. This problem is most noticeable with mods that add or edit scripts but the problem can occur with mods that do not add or edit scripts.

As i remeber, mods that add constantly running scripts are the problem. Simple plugins should be safe-ish to remove, and pluginless are safe to remove. Usually.

But to be completely safe, don't remove mods without restarting from scratch.

It is important to remember that sctripts are not the only thing getting permanently baked into a save. Therefore one might easily think mods without scripts are safe to remove. This is not the case, there's always some data permanently baked.

When you install a mod and make a save using that mod, you are committed to use it to the end.

Here is everything that is known to cause problems due to baked in save problems and removed mods

http://afkmods.iguanadons.net/index.php?/topic/3676-skyrim-information-baked-into-saves/page-1

That topic was for Skyrim, Skyrim SE may have added a few things to it not yet discovered

If you value a bug free game that will be less likely to get complex issues further down the road :

Dont uninstall mods and continue a save game .. Start a new game

Dont reorder your plugins, and continue a save game .. You should install all the mods you want, sort load order, play that setup until bored

Dont trust save game cleaners to clean saves of all issues 100% .. No doubt they clean out a fair amount of issues, but not all of them ( even the programmers will not give you that guarantee )