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.