Depends, it's more like you pay a storage company to look after your gold. A year in, the gold gets burgled. 10 years later, all the gold in the US is turned into Mercury in some bizarre freak accident, the price of gold skyrockets, and you come to the storage company to collect your gold and they go "oh, we lost it lol". I can't see a fair valuation of the loss being the time of the theft, that would only be the case if customers were told right away, keeping it a secret would be a hedge otherwise, if it goes up, no big deal, if it goes down, you make a profit.
People will have been withdrawing fiat though. So e.g. I sell my 5000 bitcoins 3 years ago, and Mtgox lets me withdraw it because they have the money covered in their fiat account. Later it turns out they never had those bitcoins in the first place (because someone stole them), so all they've really lost is that fiat figure.
Them losing 750k bitcoins doesn't mean they've lost 750k bitcoins that were currently in user accounts. Obviously, they'd be worth the current market rate. It's likely that (to some extent) the bitcoins were being covered by Mtgox's margin over the years.