Because it's not reddit (stop acting like it's reddit - the communities and conventions are quite different) and if you want to participate in a discussion, stay in the thread.
Did you come from /r/programming? There have been a few comment threads talking about hacker news recently.
You're making excuses for poor UX in a way that makes you sound elitist. Not alerting you that you have replies is ridiculous. "Stay in the thread"? No, thanks, I'm not going to keep checking my comments for replies. Thankfully there's hnnotify.
It really does, but the anti-Javascript crowd here is very vocal and would likely inspire some sort of Digg-like exodus if the UI were ever brought into the 21st century.
Did you come from /r/programming? There have been a few comment threads talking about hacker news recently.