yes they are, but that doesn't mean that you as a user can extract any meaningful information from them. Where comments show up on a page is a function of time, scores and average karma per post of the poster. The main trunk of a debate will be somewhat navigable by this metric, but the subthreads won't.
I did a back of the envelope calculation here: http://news.ycombinator.com/item?id=2569997 that shows that there is no way to assess the scores of around 50% of the comments.
I did a back of the envelope calculation here: http://news.ycombinator.com/item?id=2569997 that shows that there is no way to assess the scores of around 50% of the comments.