First of all, the coins on Cryptsy don't disappear.
When a coin is paused for trading the customer's access to the paused coin's wallet is temporarily suspended. This is for the customer's own security. The coins don't go anywhere and are still safely kept in the protected wallet.
In terms of why it's not trading, Cryptsy prefers to err on the side of caution and because of our current network situation they must have decided it's best to pause trading for a bit. We're now in contact with them and keeping them abreast of the progress being made with the software patch.
Please hold tight and rest assured that we're on the job and almost ready to release the update.