If you restore from a backup, then the folders probably get restored. If you did a clean restore (ultra-extreme solutions) they should all be deleted.
Now, if you were to turn off Photos in the backups, then backup, and restore that backup, it 'should' delete everything. Of course that's all photos, not just the ones you wanted to delete.
If you decide to use the new iCloud Photo Library (when it's ready) that would become a non-issue. They would sync back.
Anyway, what method are/were you using to copy the photos off the iPad? If it was using the DCIM folder on a Windows computer did you then delete those photos directly using the computer? I consider that an iffy thing to do, and one of the results might be ghost photos and folders that you can't delete.
It is fine to copy photos off the iPad by that method; however you should always delete them from within the Photos app, if at all possible; and you should never add photos directly to the DCIM folder.