If you are indeed talking about large withdrawals the reason could be their cold storrage. Any reasonable big amount of coins should not be storred online. A securitiy machanism for this storrage could make withdrawals only possible every 12 hours (e.g. need confirmationd of at least 2 out of 3 possible people)
I don't know if cryptsy has a cold storage. Probably that's not what OP was talking about. But if coins outside of the exchange are traded inside it, isn't this close to fractional reserve too?