Iirc the vita will not ask for an update even from the ps3 after doing some stuff involved with qcma I believe. I cant seem to find any sources somehow. Ill keep looking but im like 80% positive its possible to avoid those update messages.
It's alright, I just turned my second vita into a PSN slave and use that to backup my games then transfer them to my other vita via QCMA on the PC.
Though, if you happen to figure this out, perhaps it'd be nice for people who don't have two vita's lying around but want their psn games.