Players come to Notre Dame because ND prepares them for a career after college better than 95% of other D1 schools. That is whether their future is in professional football or in the work force. Niklas spent 3 years here, found what he was qualified to do, what he would get paid a lot of money to do, and he took it.
You can say, "Oh his draft stock would have been higher if he came back for his senior year", but that's not necessarily true at all. We saw our D-line get obliterated with injuries that could potentially hurt Nix's draft stock. Te'o might have gone higher in 2012 than he did in 2013. A lot of players come back and see their stock die.