My question is why do you need any bitcoins at all in hot storage?
What's wrong with netting until the end of the day and then put the required amount of coins in a hot wallet to do settlement say 24 hours after a trade?
Wouldn't this cooling off period give software and risk managers a chance to find invalid transactions and keep funds from being stolen out of a hot wallet?
In the Bitfinex case essentially all bitcoins were in hot storage. Why they switched to that system I don't know. Perhaps they were convinced by BitGo marketing brochures that this would be more secure. Or, they were forced to do that by regulators.
In the general (not Bitfinex) case, you need hot storage in order to process withdrawals quickly. No one is going to use a cryptocurrency exchange which makes you wait 24h to withdraw, this is unacceptable in such dynamic markets.