If BTC-E will have problems, then it will also hit hard on LTC price, since it's the biggest market for LTC.
I converted my LTC to BTC and transfered to stamp. I have always been nervous on keeping money in BTC-E, because their lack of transparency. They have a great interface and engine, but sadly I don't trust people that I know very little of. So, their confidence that everything will be fine won't make me very confident. Suffered a small loss because of this move, but I think that it was necessary to avoid the risk. I'm afraid that LTC price will drop more and there will be a lot of FUD, before it's known if BTC-E is in fact in trouble.