Because it is easier to create slapstick than meaning.
Humor may be a part of life and discourse, but in certain cases, and especially on the internet, it distracts from the real issue at hand, as most slapstick fails to convey meaning. If you can make me laugh and then think, then more power and karma to you, but most of us are unable to produce such witty insight on the fly all the time. We try. We fail, and we spam. That's why HN doesn't like slapstick jokes. If one person starts using slapstick then it creates a chain reaction that distracts from the real issue at hand.
Such slapstick doesn't create meaning. It ends up destroying it.
Except that it at least prevents the discussion devolving into a long chain of jokes, like you see on Reddit, and generally keeps this kind of thing to a minimum overall on HN.
There's a place for those chains of jokes, and that's mostly on Reddit (which I enjoy browsing often). But I would prefer to keep the discussion here on HN a bit more meaningful.
I think mkr-hn's point, though, is that Reddit may have joke chains, but HN has "tell-people-why-they-should-not-joke" chains. They're probably both equally time-wasting (this whole thread is a good example, and yes I'm aware of the irony of adding to it. Shit happens.)
I don't want to speak for him, but I'll give my opinion of why:
Reddit tends to be overrun with memes and jokes, and HN has always been more about lively discussion and facts. Reddit used to be like that a couple of years ago.
I like good jokes, but when I want some, I go to bash.org or the like ('Humour' folder in my GReader has more feeds than 'Technology'); but HN is not for jokes, it's for good discussion, so let's keep it like this.
I think you might be right in that... unique humor is rare enough that it certainly doesn't threaten to overwhelm a site, and it might even represent an increase in overall conversation-intelligence.
Memes, on the other hand, are repeated endlessly. Perhaps still funny, but it's the repetition that drives people away and dumbs down threads, because it contributes literally nothing, but it does distract. It also turns the place into an echo chamber - others were very likely thinking the same thing - and group-think is dangerous.