According to a Japanese English-Language newspaper, one of Gox's lawyers is saying that the coins disappeared during the ddos attacks that took place in the days just prior to the shut down.

If that's the case and the coins were moved, there'd be a significant spike in the BTC days destroyed. The only spike is on the 8th of March. This was attributed to a movement of just 200k coins. (I think thats what I remember reading - please correct me if I'm wrong). That would be a good place to start looking, if I could make any sense of the unintuative blockchain.info

But an alternative theory which is more supported by the blockchain data (insofar as I understand it) is that the keys are some how lost/stolen and the coins are still in place. (or MK stole them, or the Feds/NSA took them, depending on how pointy you fold your tin hats).

Edit: P.S. Hats off to all of you contributing a reward. Really good things to you all.