Comentário oficial
You can use any number or sub-folders and then simply drop the parent folder into rekordbox - it will only find the new files and ignore the rest.
If it comes time to move the drive / database to a new computer, when you relocate, you can MASS relocate because the structure of the folders doesn't change, just the location of the parent folder. Eg.:
Old: X:\MyOldDrive\Music\Folders\Files
New: Z:\MyNewDrive\Music\Folders\Files
The difference between the two is everything to the left of "Music" - relocate one track, tell it to relocate ALL tracks using the same shift, and presto.

You are prompted to locate one of the files (sometimes the first, sometimes the last in the list), manually locate it in the Explorer or Finder:

That's it.