At MtGox, it should be much simpler to (1) add up all customer balances, (2) add up all BTC in hot and cold wallets, and (3) compare those two numbers.
If the numbers differ by more than timing differences, shut it down, debug it, and prevent a small problem from becoming a big problem.
The Barings backstory is that the billion-dollar loss started with a 20k bad trade, Leeson tried to cover it up, and it snowballed.
It wouldn't be surprising to learn that MtGox followed a similar trajectory.
Yes, considering Gox only had 2 bank accounts (and now are down to just 1 in Japan) I don't see how hard it is to compare balances and notice 744,000 coins are missing.
They claim that over time the cold wallet was cleaned out. If this is true then the first few customers would've complained hey I never got my coins, and he could've seen shenanigans happening due to his php wallet implementation and halted all trading. Then thousands more customers. I find it hard to believe 744,000 worth of coins disappeared over months and nobody noticed until recently
The history of Barings Bank is interesting, primarily because the main trader Nick Leeson was in the position to mask hundreds of millions of pounds of losses. In that case, no one noticed the roughly $1.3B loss because he was in a position where the internal controls didn't apply