Among other things, HN was a test case for programming in Arc, and mostly by one programmer: pg.<p>So the likely reason that HN does not allow Markdown is because there is/was no Arc implementation of Markdown.
What extra formatting would you want? And why? To some extent, fancy formatting only detracts from carefully reasoned arguments. Why clutter the page with more layout?<p>What would you use, and why?
I'm not certain but I think its because HN wishes to promote positive up voting not down vote trolling like reddit etc... If its good It will get up voted, if not then just don't upvote it.
The point of markdown is that it's supposed to be perfectly readable in "unrendered" form, so in a sense you can already use markdown in any plaintext context.