Basically what I thought it would be. As I understand it, Cryptsy kept most of their coins in cold wallets that were separate from their servers; probably on flash drives. Very little of each coins actual currency was kept on the main servers. This is why when you tried to withdraw large amounts of some coins it would take a while for the order to actually be processed... Or they were employing fractional reserve methods and had to locate enough coins elsewhere to fill the order. 

Whoever made off with the cold wallets, escaped with most of the users coins.