What I would suggest, to be on the safe side:
1. Create special folder inside LR called "0 files" or something identifiadle.
2. Drag all the folders which contain 0 lightroom-managed files into that folder from within lightroom.
3. Go ahead to check the real emptiness of the folders to be deleted via Finder, ForkLift or anything else.
4. If you have no files there that you want to keep, or all the folders are really zero, delete them from lightroom.
5. The folders that have something will still be on your HDD, not spread over your entire file system but in one location where you can easily find them. So you can manually delete the remains of "0 files" folder with the folder itself.
If you don't care at all about the files that may be left over in these 0-folders, skip step 3. On step 5 just delete "0 files" with all included subfolders
The most time-consuming part is to select all the empty folders, which will take you for 100 folders around I would say 3–5 min.