http://www.reddit.com/r/Bitcoin/comments/1z37zw/mt_gox_has_at_least_200k_btc/ Looks like the blockchain indicates that Mt. Gox sill has between 200k-400k bitcoins that havent moved since 2011. So he possibly either lost the private keys, or he put them in the bank and the government might be blocking him from getting access to his safety deposit box and they put a gag order on him at the same time so he couldnt tell people what happened.
Very plausible that formal banking institutions, FBI, CIA, US or Japanese gov put a hit on the dude or denied him access to all these private keys. They definitely didn't disappear in thin air! If they try to regulate BTC to death it's going to be hard to put a blanket over all crypto currencies because a bunch of them have different properties and ways in which they can be used. IF BTC gets regulated to death or whatever Litecoin will replace it ect ect. The tech simply cannot disappear it's like un-inventing the internet. (if that is even a word) Like I said in a different thread, I think losing net neutrality would actually be the biggest threat but there are many solutions being created to solve that prob as we speak so I am confident this technology will survive.