I've updated a few apps through there and they still work, but it seems apple knows if you have any of their products installed regardless of little snitch, I'm sure the update scan sends back data to apple which I'm sure is suppose to be anonymous so they cant really prosecute unles they admit without breaking some privacy laws
This mainly pertains to Apple software that requires install keys (primarily the Pro apps). Since the software is recompiled it has an updated list of invalid keys. Usually apps like iLife continue to work just fine.
They dont monitor the apps over the web like Microsoft and Adobe (at least not yet).

