I upvote as soon as they're in good faith (which, fortunately, almost always are on HN, compared to something like Reddit.)
I wish to encourage conversations I am interested in (or I otherwise enjoy / appreciate). Bothering to write a reply in good faith is nice.
Also, internet points are a worthless, sham, game-ification trick thing.
Using upvotes to indicate "I've replied to you" is also going to be drowned out by noise because a poster has no way to know who has upvoted therefore no way of distinguishing your "I've replied to you" upvote from a regular user who upvoted their reply because it was informative/useful.
While I fully agree, it works well enough as is :)
One view could be that the purpose of upvoting is to lift informative posts to the top and make them quicker to find. In that case, I don't see that downvotes really add much. Poor posts just sink to the bottom from lack of upvotes.
Another view could be that the purpose of voting is to show dis/agreement. My own feeling is that expressing a position without offering a supporting argument is a bad practice. Others no doubt feel differently about that.