[Windows 11]
I’ve created 100 subfolders in one of my vault folders using Explorer. Opened Obsidian, went into that folder and:
- add two folders,
- remove one folder and
- add some notes
No problem. Was using two characters for folder names. By default, on Windows, the path cannot be longer than 260 characters, but through the registry, you can extend this to approximately 32,000 characters. (Could be that it’s some company policy.)
However, be cautious, on a C: drive (or whatever your Windows root drive is), you can have only 4.294.967.295 folders. 
Cheers, Marko 