The .AppleDB folder is a special folder specifically used for AFP support - CIFS access is configured to hide this folder as it should never normally be played with and is not needed for CIFS access.
You can try connecting to the share via FTP, or SSH if you have that enabled, and delete the folder that way.
Note that if you have any aliases or mac-specific package files that you work on directly from your NAS, these may be impacted by deleting this folder, in which case I would strongly suggest you have an up to date backup before doing this
NAS: Ultra-4, NV+ & Duo v2 :: ST31500341AS & HDS723020BLA642 Drives
Network: Netgear GS108Tv2 / DM111P :: Airport Extreme / Express & Time Capsule
Clients: OS X 10.6 - 10.8 :: Ubuntu 11.x :: Win 7 + SP#1
UPS: APC ES-550