HN allows duplicate submissions of stories that haven't had significant attention in about a year. We want good stories to have multiple chances at making the front page.
Our goal is to optimize HN for curiosity and the front page for the best stories, and it's fairly random whether or not a good story gets traction the first time it's posted. If we were anal about disallowing reposts, sure we'd get a more deduplicated submission history, but we'd also end up with a poorer front page. Bad trade.
There are things we're working on to reduce the number of dupes that are appearing. The problem is trickier than it seems, but we'll get there.