The feds could have transferred his BTC to another wallet. Your backups are of no use when the blockchain insists that those Bitcoins don't belong to you anymore. Correct me if my understanding of Bitcoin is wrong, please.
As for the hacking charge, I'm not sure - but you can read the court docs here - http://www1.icsi.berkeley.edu.nyud.net/~nweaver/UlbrichtCriminalComplaint.pdf. I still need to go through this myself so I won't comment on why there is a hacking charge.