What happened here is common in business bankruptcies. Initially, the old management wants to stay in control.  They often think, if only we had a little more time, we could get out of this hole. Something great will happen. ("Bitcoin will go to the moon!") We'll find a buyer with deep pockets. (The guys who wanted to pay 1BTC for Mt. Gox don't qualify).

But it usually doesn't work that way. More often, things get worse, the courts send in bankruptcy pros, check out the situation, and report back that there's no way out - this is a dead company. So the court sends the case to liquidation.

If there's fraud involved, this is when it starts to come out. The old management has been fired, and a bankruptcy trustee is in full charge. Bankruptcy trustees have seen it all before. When there's a lot of money missing with no good explanation, they get suspicious. That's part of their job. They have all the authority they need - all the remaining employees now work for them, the business records are all under their control, they can bring in auditors and experts, and they can get court orders from the bankruptcy court.  They can ask the court to "pierce the corporate veil" and act against the old management. They can undo insider transactions involving transfers of assets out of the company.  They can also file criminal complaints with police, or ask for a police investigation. The trustee has all the tools needed to find the missing money.

The supervisor in the Mt. Gox case has already mentioned that they're bringing in outside experts and are talking to the Tokyo police. There's clearly an investigation underway. I expect more of the missing funds will turn up.