My bet is that the coins where either lost a long time ago or stolen by insiders. Whoever is responsible will probably get away with it though, because they will blame it on "faulty bitcoin code," and the investigators won't know enough to call out the BS. The only real evidence will be the log of all internal transactions, if that even exists. But that could be fudged also. At the very least though, MtGox would be guilty of some kind of commodities trading fraud, or the equivalent term in the Japanese legal system.