Dude. All exchanges use a pooled wallet. There is no such things "your" BTC or "your BTC" wallet on BTC-E, MtGox or any other exchange. The exchange simply has one (or more) hot and/or cold wallets. Then they maintain a database of each user's balance, and trades change those balance. One could withdraw "fake" BTC just as easily as selling "fake" USD for BTC and withdrawing that.
The likely reason for faking USD is simply because that is the exploit the hacker founds. Hacker found a way to add USD to his USD balance. Once had had that why try hacking any further. Give yourself huge amounts of USD, buy BTC and remove them from the exchange.
New theory: hacker emptied the BTC-e BTC wallet first and all that's happening now is him having some fun with the other users..