FBI haven't found the servers probably, yet. They only got one admin. They'll make him squeal. That's very easy. 2 choices.
Why do you think that they haven't located their servers?
Cloudflare must know btc-e ip addresses and US can easily get those address from Cloudflare so they are aware where their severs are. Anyway their mt4 servers are still online but logging is disabled.
If that is btc-e owner is really arrested then they must arrest managers of Mayzus Financial Services Ltd too because they were the ones doing actual money transmitting.