None of those directories have anything to do with Rockbox at all.
It pays to note that removing Rockbox itself wouldn't have removed these directories either*. Anyway, moving on.
These are created by the original firmware, and should be recreated at runtime. Boot the original firmware, and they should be back again. Their contents, however, unless backed you backed up, are toast.
[Saint]
(*depending on how you chose to do this.)