This was a known issue in 10.7 and 10.8, but should be fixed in 10.9. For your app, you probably shouldn't worry about it. Manually tweaking clients.plist
requires root and is a lot of work just to prevent an entry in a prefpane most people rarely use.
Your users can follow the guide at https://superuser.com/questions/526183/remove-applications-from-location-services-in-security-privacy-on-mac-os-x-10 if they really want to get rid of them.