They take on more coins than their system can handle because they, just like the modern banking system, are fueled by greed. I have been using other exchanges instead and I have NEVER had a single problem with any of them, even the newer ones, which says it all.....
Cryptsy has a lot more volume than the rest. It is King of the altcoin market. I can't think of any exchange that get anywhere near the volume. The problems started when volume began to increase.
Cryptsy is guilty of adding too many idiotic coins, and not employing people technically capable of putting together a site that can handle the traffic.
I owe them 10 LTCs apparently, which I don't intend to repay.
Oh, and I once logged into coinex to find nearly 2 BTCs in my account. Not mine. But then it wouldn't let me spend them so no harm done.