That's insane. They were forced to change their business rules after the Gox collapse, but this says a lot on how they operated, even back then. I would hope their operations changed a lot since the Gox collapse. I also wonder how much they lost on Gox, and have been running on a fractional exchange ever since?
I wouldn't be surprised if they had half the coins in Mt.Gox because of the rapid trading and so that was happening on that site; because you have to keep in mind that there is no need for an exchange to have coins sitting there idle, and they are allowed to do whatever they want once you deposit. Chances are they had some folks doing rapid trading to make some money with high numbers of BTC.
As for Bitfinex's operating practices, I don't know what they do, but if they were able to go from then until the hack without facing any scandals or anything, then they must have been doing something right.