Oh man does this bring me back to my high school days
. We had a 1:1 program and the students always seemed to be two steps ahead of Laptop Central.
Anyway, if he was signed in on the same computer around the same time, then yes, there's a chance he did it. A pretty good chance actually.
Depending on how the system works, you might HAVE to sign in to even access ANYTHING. Hacking doesn't happen out of thin air... there are procedures that have to be followed to get to the exploits.
You saying this being like being on the same block as a crime is sort of inaccurate. If he was simply in the same computer lab as the computer that did the hacking, that would be a little more accurate.
I think you need to get their full story, as well as your son's. When I was in high school, the computers tracked our every move. Hopefully yours do too.