They can just launder those coins in the altcoin market. It is possible that they were stolen from him by someone close to him (if he really doesn't own them).

Developers, stuck without direct access to the Mt. Gox source code, resorted to playing video games, people inside the company at the time say. Employees were also concerned that Karpeles' tight grip on all company affairs was causing a bottleneck: he was the only person who could access the exchange's bank accounts and bitcoin holdings and resolve requests by traders to cash out. Former employees say they asked Karpeles to share the passwords to Mt. Gox's bitcoin wallets in case he became incapacitated or unable to access the data. He refused, leaving him as the only person able to piece together the passwords, written on paper stored at his home, the office, and an undisclosed location.