It's pure speculation, but it is a possibility. The addresses that Gox at one point had access to still have a sizable chunk of bitcoins, so that rules out the possibility that all of Gox's bitcoins were stolen or lost because of the transaction malleability bug.

This opens up the question of why Gox hasn't signed a message with the private key for the address to prove that they still have the bitcoins. One possible explanation is that they lost the private keys, but there are many other possible reasons.

I think the theory is that he no longer has access to the keys... the implication being that the authorities are in control and he has to obey a gagging order.