It wouldn't even have to be a judicial order. The FBI or Treasury Department agent could just tell him something like "keep quiet about this or you're looking at 10 years in a federal prison". This is how prosecutors work here in the U.S., and Mark is under investigation by the U.S. government.
I don't believe this is right, but this is the reality.
Why is it so unlikely that they seized more money, probably in the form of paper wallets from a safety deposit box? Japan law enforcement works closely with the U.S.
But here's what they really wanted from Mark, and I wonder if they got them: all the Mt. Gox account records, including IP logs and bank account numbers.