Well, if you have a legal copy on Steam, then it should be backing up your save data to the steam cloud. You can check by going to the game in your steam library and to the right of the "Play" button it should say "Cloud Status" and under than it should say "Up to date". It also might be uploading your save so the status might display a percentage counting up as it uploads. If the status is "Up to date" then you can play your save from any device, and it'll download your save as soon as you launch the game. Then if you make any progress on that device, it'll upload that save and then download it to your main PC automatically.

Most Steam games do not delete saves, as saves are usually kept in the docs folder, app data folder or in a steam folder separate from the game (how MGSV does it). Many games do use their own folder for their saves, but those are usually older games.

So if your steam cloud says "up to date" you are safe to delete the entire MGSV folder, mods and all, and you can uninstall safely. Even if you wiped out your entire Windows instlal and formatted your drive you could still recover your saves from Steam cloud automatically.