You should only organize things as you actually use them. The things you use are then generally organized and you haven’t wasted a bunch of time organizing stuff you never use.

If you do decide to organize a bunch of stuff you never use, that decision is then totally aesthetic, so you should choose a method of doing it that you find aesthetically pleasing.

Source: obsidian user who spent a bunch of time organizing stuff he never uses.

I largely agree, that's why I've still got all of it stored away, but I guess I'd like to keep track of what is it that I'm not using, what can I delete and what can I deduplicate.

Not the answer you're looking for, I know, but I used to have 100+ labels/folders, 4-5 deep, and decade+ old emails, obsessively organized etc.

5 years ago, I dropped down to 20 labels, and started routinely deleting anything over 5 years old except for a specific "keep forever" label.

No regrets. No instances of searching for old items and not finding them, etc.