Many of the post in HN have very few comments, so it's not strange that most subcomments are in the first few main comments.
Actually posts with few comments have basically a flat structure. They have usually just one thread with two or three comments and the others are "single-comment" threads.
It's the posts with a lot of comments that tend to have three or four very long threads and those long threads skew toward being under the first comments posted.
But discussions like this will make the first comment have the 100% of the subcomments.
Yes, you are right and that's the thing, the action happens in the first couple of thread ( this discussion is a bit meta btw ! ). The point is, it still hold true even when the total number of comments on the page is bigger.