As I said, the original copyright holder may not care. Christ, they may not even know that they own the game with all the companies and copyrights that have changed hands since the 80s. But ebay isn't going to take this into consideration. They see black and white. Legal or bootleg. Where are they supposed to draw the line and is it even up to them to do so? They do whatever they need to do to protect themselves.
And as far as money charging hands and profiting, last I remember the auction in question was over $250 for a single cart. Ask yourself this, if making money and profit wasn't the goal then why was it ever posted on ebay in the first place?
Yeah, that's right, breaking the law is ok as long as you have friends that agree with you.