They are to rank the comments and give the users karma points. So yes they have a purpose.
OP points out a real issue, though. If you didn't already know that, how would you? Perhaps some alt text could be added to the arrows.
You make a great point. It probably took me a day to figure out what "karma" was, upvotes, etc. I don't think I sent a single upvote for weeks since I didn't know how important they were/weren't.
HN isn't really set up for the new user, IMHO.
I agree. If I had never used anything like Reddit or Digg, I probably wouldn't know what the arrows meant.
I'm pretty new here (about a week I think). While the voting/karma system isn't readily apparent, like you, I figured it out about a day after registering. I think the FAQ could possibly benefit from a more thorough explanation, but I do think people figure it out eventually once they start participating.
I registered yesterday and came to know about it immediately about what he up arrows are. Anyone who's familiar with discussion forums can get it in a while I guess.
But, sure, I think HN should have given a note of this.
Using Alt text is a good idea to keep the space clean and unintuitive.
getting rid of karma points on comments has certainly hurt here... it's harder to ascertain what they are for when they don't increase.