I wouldn't say they even have hot wallets. I believe these are all manually-batched transactions. From what blockchain evidence I remember seeing around the time of the seizure, it looked like they were splitting their wallets extensively. This should make the current refunds more difficult to track.

However, I highly advise against depositing directly into, say, Coinbase. There are plenty of other services that don't have the means nor the will to freeze your account for tainted coins. Coinbase (and perhaps Gemini, Bitstamp) definitely work with blockchain analysis companies and law enforcement. If I were sending coins there, I'd mix them through a couple non-KYC services first.

It will be much easier to track BTC-e's wallets once the service is relaunched, and we see regular hot wallet procedures, including the pooling of incoming deposits. I'm curious to see if fungibility issues arise.