As far as i am concerned there hasn't been any issue with sync trophies of pirated games, i know cause i have JUST ONE trophy for it. But to be fair, i doubt they can proove is pirated since the game exist in physical form.
Just for the record here is a example. Dead or alive xtreme 3 is a game only exclusive to the asia markets region. But is able to be bought in physical form, and the vita isn't region locked (i think) So who is to say i didn't buy the game, and playing it legit? Sony wouldn't know if i did or not. Can they proove i did pirate the game? No, cause who to say i played it one aay, didn't like it and gave it away?
What they can prove and should be worried about is games exclusive to playstation store. A game like for example, Dragon fantasy or retro city rampage can only be bought from there. So if you have trophies for a game that you didn't pay for, that is supicious, sony can see on your download list what you have access to and having trophy data for a game you cannot download (Cause it wasn't bought from playstation store) Shouldn't appear on the download list and you shouldn't have trophies for.
I have thought that just like on ps3 or ps4 where you can download a game, and have different users play the game even if they didn't buy it. But that is on ps3 and ps4, my brother play some the games i buy on his profile using his psn so is never a problem. But i dunno if the vita is the same way, unless someone knows better than i do. To my knowledge the vita has no profile system for multiple users like the consoles, so i dunno, maybe? Try it and see yourself if you can log into another psn from the system and still play games from it, (that is the games don't block you for not having access to the psn account it was purchased with) If it works then is probably nothing to be worried about, since is unlikely sony can prove you or anyone pirate the games just by clues of trophy data alone.
(Yeah i thought this out, but is just speculation) If it really bothers you and you wanna be careful, then you can either try not to sync trophies by logging out of psn in the settings app before playing any games, and if you need to log in for some reason (At the point of typing you can't cause of spoofing inactive) then somehow delete trophy data or avoid sync whenever possible.