Rockbox isn't picky at all about this kind of thing.
It doesn't expect any particular arrangement of files or directories, with perhaps the exception of /Playlists (and possibly /Recording), which it will create itself if required. It has a full file browser with a user settable start location, and a database that will traverse the entire filesystem looking for media, it doesn't expect media in any particular location.
Long story short, you can delete everything except /.rockbox, if you wanted, and Rockbox wouldn't bat an eyelid nor shed a tear for their loss.
[Saint]