FBI has your BTC-e password hash, 2FA codes and your public cryptocurrency addresses!
FBI or another three-letter-agency can use this hash to find out your password and crack your account at another exchanges and websites!
Also they have your e-mail address. You may consider changing it or securing it!They may try to crack it!
Do not reuse your password! They may try to find your password using dictionary attack. This is why you should not use words from a dictionary.
If BTC-e become operational again you have some chance to withdraw funds before FBI to crack the new BTC-e website!
American three-letter-agencies cannot be trusted!
Maybe NSA will try to steal from you. Or another American agency will three letters. Or another American agency (with less or more than 3 letters in their name).
Also corrupt agents may sell the database. Like the agent that stole coins from Silk Road.
They have access to list of your public cryptocurrency addresses. Do not reuse addresses!
You should be scared now!
It will be very hard for BTC-e to verify that genuine users are trying to access their account, not FBI/NSA or other 3 letter American agency.
Maybe they will send verification codes to the e-mail, ask for cryptographic proof about user's addresses, etc.
Only genuine user can create signed message with his private key corresponding to the public key where the user is sending/receiving coins.