They never have bricked phones after an update... whoever said that was a paranoid fool.
However, whenever you update you will have to rejailbreak and unlock but that should be pretty obvious. If you updated to the very latest firmware (4.2.1) then you may run into some problems getting it unlocked again.
To answer your original Q though, yes an unlocked 3GS will work just as it always has with both itunes and the app store. I don't believe Apple can see if you're unlocked or not, and even if they can they don't really care as it's perfectly legal and you're still paying them money.