Is there anywhere else (another messaging app hidden somewhere) that could be generating these notifications?
When you get an SMS notification that isn't from the SMS app, and you open it, does it take you anywhere other than the default messaging app you disabled the notifications on?
Or, could you install GoSMS and try sending a message from the contact list (It'll then ask for the SMS app to use) and see if there's any more than the default app and the Go SMS app?
It's all good info for the OP I guess
Phone: Dell Streak Running: Gingerbread
Phone: HTC Dream (G1) Running: Gingerbread
Tablet: HTC Flyer Running: Honeycomb
Goodbye WinMo, you will not be missed!