These servers hold the data of your coins and $, so I wouldn't call it nothing.
Also if there will be political pressure, then Cyprus will bend as well. There are not many countries in that region that are immune to Russian political pressure. And remember that BTC-E isn't actually something that's very important to the country it resides in. It's just not profitable to protect BTC-E with the cost of going to bad terms with Russia.

So the main question here isn't if BTC-E falls under Bulgarian or Cyprus jurisdiction, but how bad do the russians want to get BTC-E and are they willing to go political with their investigation.