Right now, only Vinnik is indicted. BTC-e only received a fine (as far as we know).
Unfortunately, it's worse than that. BTC-E was indicted on two counts, as part of the same indictment -- running an unlicensed money service business and conspiracy to commit money laundering. And the feds seized their main domain (BTC-E.nz still seems untouched, not sure about the others). So it looks a bit more grim; I think they expected that $110mm fine to be paid out of seized funds. But it's still not entirely clear if they were able to seize funds. One would think they would have announced it in the initial press releases...
Yes, but the were not running the business in the US, and there is no mention of a take down order which would only be enforceable for companies under US jurisdiction. To take someone else down overseas requires the action of local authorities, the US are not going to raid and snatch things in another country without a political uproar.
What I think is most likely is the BTC-e hosting provider was US owned and took them offline so they are looking for a new provider.
If BTC-e have instead decided to close up shop and do a runner, which would be a bad thing to do as it's an admission of guilt, then the chase begins.