I just use Namecoin-QT. I do not trust leaving any quantity of anything at BTC-e or any other exchange unless I'm actively trading. I don't like using the exchanges as wallets. This attitude of mine predates the troubles at Mt. Gox, but that just strengthened the view. I've also had instances where BTC-e in particular stopped all BTC withdraws for a few days, and other instances where they take an absurd amount of time to make the transfer. They have a high transfer fee, and it is't because they put it towards your transfer. It's another way they charge you. I assume the use the lowest possible tx fee possible, apart from sending it with no fee at all. I'm sure your NMC would be relatively safe. I'm just giving you my opinion, since you are asking about it. At least you can encrypt QT. it's just password encryption, but it's something. With BTC-e, you can add 2-factor authorization for the site, but you have not control as to what they might be doing with it on the other side. I trade there, but can't say that I have a lot of trust. I never transfer fiat to them, and only trade with small quantities of BTC unless they flake out. Oddly enough, they're one of the more 'trusted' exchanges.