If you're running an older version of ShutterSnitch (prior to v4.7) this is the way to do it:
1. On your device, go to the home screen.
2. Connect the device to iTunes and upload a file named "resetpassword" to ShutterSnitch using the Apps > File Sharing feature.
3. On your device, open ShutterSnitch and you'll be asked to put in a new password.

The "resetpassword" file can simply be a empty textfile saved from, for example, TextEdit or Notepad.