That can be a problem with sites like this, but it hasn't started to happen yet here. I watch the site quite closely and I haven't started to see good stories slipping unseen off the new page.
It is a major problem with reddit, and could possible over time become a problem for news.yc, but it is not necessarily an insurmountable problem. For instance, if you really get a lot of submissions, you could pre-select probably-interesting posts with a text classifier and shunt them into a probably-interesting queue. (A text classifier could be something like the ones used in spam filters, or, if you want, you can throw the whole machine learning book at it and use Markov chains, neural networks, &c.)
If Paul Buchheit were reading this thread, he would say that pg should focus on more immediately important things first, and only when it becomes a real problem come up with a way to tweak karma to disincent posting lots of irrelevant links. Except Buchheit's wouldn't be a run-on sentence.