I mostly agree with you, but it's not hard to create a karma system that isn't just a reward for hyperactivity. For example, Hacker News could change its system so that nobody got a point simply for posting a comment.
But however fine-tuned the system, no point system is immune from gaming, and no-one can expect points to be any more than vague clue as to someone's true worth as a participant in the community.
Karma/Reputation systems on website are to reward a desired behavior. Part of HN's value is it's active useful conversation (vs /.,digg etc). So it makes sense to give the community the tools to reward what they want and create positive self feedback. (Also like the other reply, simply posting doesn't give you karma)
There are two problems with what you say. First, a large number of posts with a small number of upvotes is still valued more by HN than a small number of well-respected comments. Second, moderation systems tend to be inflationary, which means that the point value of a given comment has more to do with how many people read the thread than anything else.
Slashdot's point cap is the obvious solution, but even there comments tend to lean heavily towards +5 on well read threads.
Re: first problem: I think a large number of fairly good comments probably IS a more valuable contribution than a small number of very good comments.
The second problem is more, er, problematic, but you could argue that good comments are popular articles deserve more karma, since these are comments on topics which people are really interested in – i.e. valuable insights on hot topics benefit more people than valuable insights on obscure topics, and are therefore more valuable contributions.
I agree that voting systems on the web end up favoring the most persistent, rather than the most worthy or highest quality. This is something that I've seen on Wikipedia and Digg. And to an extent with the trolls on Kuro5hin.
I think moderation is important, but that it should not be the central aspect of user interaction.
But however fine-tuned the system, no point system is immune from gaming, and no-one can expect points to be any more than vague clue as to someone's true worth as a participant in the community.