My funds were in USD. Does that mean I'm safe even if bitcoins were stolen?
It all depends on how BTC-E is going to handle a potential theft of crypto funds ~ in recent examples we have seen that exchanges tend to generalize losses by giving every user with a balance a haircut worth an x percentage.
I have around $300 in fiat stuck there, which I obviously want to get back, but there are people with tens of thousands worth of funds, or even millions, that are now desperately waiting for good news.