Drives me insane, too. Apple has always had the tendency to assume the user doesn't understand the risks and consequences of doing things it doesn't like, which is absurd to me. Get out of my way and let me hang myself if I want to. Anyway... I found something that may help, though I'm still testing it out to see if the change sticks.
Note to anyone who stumbles across this: DO NOT DO THIS. YOU WILL KILL ALL THE PUPPIES. If you actually understand what I'm describing below and realize that tweaking internal system settings can result in HORRIBLE THINGS HAPPENING, well, you'll understand why I added this note. DON'T DO IT. (Or, ya know, whatever.)
Take a look at the output from `defaults export com.apple.ncprefs - | grep -2 diskspaced` -- com.apple.diskspaced is part of the StorageManagement framework, and can be found at /System/Library/PrivateFrameworks/StorageManagement.framework/Versions/A/Resourc es/diskspaced.
I tried toggling notifications for one of my apps and watching the flags value for it, but (seriously) after changing notification settings then changing back, the flags value is not the same. So, I have no idea if changing the flags value will actually result in no more notifications, this is wildly outside normal documented stuff to dig into, but hey, if you're up for doing things that will upset half the people who replied to this thread... 🙂
I set my com.apple.diskspaced flags to 4117, based on values I found for other disabled apps. This is probably entirely wrong, but worst case scenario it just doesn't stop notifying. Kinda hard to imagine notification center not gracefully handling an unexpected value here, seeing as how that's Developer 101.