I sincerely doubt that any exchange uses individual cold storage wallets, the overhead would be too big: Every time an offer is matched on the exchange or somebody wants to withdraw money, the individual wallets of the involved parties would have to be imported from cold storage and then recreated.
On the other hand, if an exchange only used a single address for cold storage, if they ever had to import it, all money would be online at the same time. That would be very insecure.
It might be feasible to sign transactions offline and then safely transfer those via mobile data storages. The offline computer would have to be made aware of the current state of the Blockchain regularly though, so, on the other hand the blockchain would have to be transfered to it manually as well. The problem I see with that would be that withdrawals would be extremely slow, or you'd have to have people running USB sticks 24/7.
I would assume that every exchange uses many different cold storage addresses. If I were to create a scheme, I would reroute all deposits directly to cold storage upon receival, and change the cold storage address in use whenever a pre-determined cap is reached. I would only store an amount on each cold storage wallet, that I'd be comfortable to have in my hot wallet at one time.
I would then keep a small amount of crypto currency in my hot wallet, in order to automatically process withdrawals. Whenever the amount in my hot wallet runs low, I would import the oldest cold storage address.