The only exchange that had been hacked and were able to recover were poloniex, i do believe they had paid already all the funds taken in the past, nowadays security is their main concern, others as bitfinex hasnt a license to work as some had reported, soo you choose where you wanna to risk your bitcoin at reputable or at others.
Poloniex is not the only exchange that refunded its users. As far as I remember, BTC-e also refunded users of a minor security breach.
In both cases the funds lost did amount only for a fraction of the funds held. Therefore it was easy to do a refund. So users have been lucky.
I don't think that you truly can distinguish between "reputable" and "other" exchanges from the outside. An exchange is only "reputable" as long as it is not hacked. There is never a guarantee that the system is as secure as it is claimed to be and that all employees are honest.
So it doesn't matter at which exchange you store your funds, you're still taking a significantly higher risk than storing them in a private wallet which you control.
ya.ya.yo!