EDIT: And I think there was a major code rewrite at around the time it was sold too.
There was also the hack that happened in June 2011 as well which was what led to the 424,242 BTC transfer in the first place. I wonder if it's related.
I have been wondering about these issues also. As I recall, the main trading engine was replaced after the crash in 2013. Prior to that time, was the exchange using the Satoshi client for a backend? (Thus slow RPC calls and easily overloaded.)
Speculation here, but what if during the 2011 hack or its recovery, someone obtained a copy of the wallet files corresponding to the hot wallets? Rather than simply stealing all the BTC in the hot wallet at that time, they realized that they could now predict the future wallet addresses and private keys that would be used by the exchange. You could perhaps generate the sequence of keys, since it is a pseudo-random number generator, and watch the blockchain for when the addresses accumulated enough bitcoin. Then use the private keys to transfer bitcoin to other addresses.
Under this scenario, you don't have to have continuing access to the exchange. And MK may have thought the old hot wallet files didn't matter since the old addresses wouldn't have balances anymore.
The fact that blocks of 100 BTC or other denominations were moved onto other exchanges, and even Mt. Gox, does suggest it may be possible for law enforcement, with subpoena power, to figure out who controlled those accounts and where the cash went on subsequent withdrawal.
All of these problems would have been caught early on by consistent reconciliation of the book balance of BTC against the wallet balances on the blockchain. This is like Finance 101, but it appears that MK did not do this simple step, which would have caught the losses at a much earlier stage.