What percentage would they have kept in hot vs cold wallets, approximately, do you think?
It's very difficult to say, as there is no way we can look into how BTC-E structured their cold/hot coin ratios. In general, and that's more an estimate of how previously hacked exchanges have divided their different storage forms, it would be something in the range of 25% hot wallets, and 75% cold wallets. Ultimately, and that's the worst case scenario, the cold storage ratio should never be under the 50% level.i hope they still have control of the cold wallets, but how do you know? any movement we see on the blockchain could be the btc-e admins OR the feds. either way, this is a shit sandwich for all involved. i had a little dough there, waiting to buy back, i consider it lost. sucks. 
It's impossible to know for sure, but the good thing is that there is no clear indication of where BTC-E is located. And even if that was the case, the funds BTC-E has locked into cold storage could be sitting in a whole different location. I am a victim as well; +$10,000 in fiat, and +5BTC is very likely never going to be seen again by me.