Hopefully BTC-E like many company are storing bitcoin in cold wallet out of datacenter server... i'm assuming FBI seized datacenter of website, they definetly seized the hot wallet... but there is hope btc-e have backup out of datacenter...
I hope they have backup... if so there is hope for bitcoin to be refunded, or website be backup... if they truely didnt arrest real owner...
I hope that most of the funds were in the cold storage, and at least 50% of what is owned to the users could be returned to them (I myself lost around $300). But are you sure that they are still in the possession of the user data? I heard that the FBI seized that as well.
Judging by the 66k BTC wallets that were moved, and the tagged BTC-e ETH wallet, I'm guessing most of the funds were indeed in cold storage. What we don't know is how much exposure they have to frozen fiat funds (they announced that Mayzus froze their accounts). And even if they still have access to most of their fiat funds (if they were well-hidden through various shell companies in less-US-friendly regions), they would have a very hard time moving any of that to customers. So, even if refunds happen, who knows how it would work?
They are definitely in possession of user data. They confirmed that they have access to their databases and wallets. The FBI did seize servers that contained those, but the exchange kept back-ups, and the wallets should have been encrypted.
Meanwhile, the FBI is scouring the servers they confiscated, connecting the dots between all the rogue nefarious actors in the crypto space: