Connecting his laptop to an Ethernet port (not intended for passenger use) is enough for the FBI to consider prosecuting him, even if he didn't actually do anything else.
Only if you can actually access the flight systems from the entertainment console, which you can't. We would have already heard of a massive undertaking of securing against this vulnerability on every 747, which didn't happen. Either the airlines have been negligent or the FBI has made up a story for a fishing expedition (most likely).
You'll notice that interview with the FBI happened in February, after he gave a talk on airplane security, and this incident was in May. Apparently, whatever he said during that interview wasn't enough to get him in any trouble.
Right, but that helped to justify the warrant. Even if he's never charged, he's lost a bunch of gear. Even if he gets it back, it will not be trustable. And any plaintext information therein may hurt him.
But maybe they asked him point blank if he had ever pwned a real plane in flight. And he didn't didn't want to risk lying to an FBI agent. Tough call.