Pre ignition, timing too far advanced, will burn a hole in a piston. Vacuum leak isn't a big problem unless you're trying to get a smooth idle. A big vacuum leak would make it run lean and hot, but I don't know if it would burn a hole in a piston.
I would bet it was a bad booster or even a good booster drawing on the back 2 cylinders. I have no idea why this happens. It might be that the vac for the booster causes it to run lean but I cant see why this would hole the piston. Could also be a small part of a plug that got in there.
Don't remember off the top of my head what symptom points to what but the type of hole it is can be telling. A hole that looks like it was punched out (fractured edges) vs. a hole that looks like someone took an acytelene torch to it.