The HN comment system discourages depth as there is a relatively shallow limit to threads. There also is no in-built concept of an inbox to monitor replies.
Hacker News prefers quality over quantity and signal over noise. Deeper threads tend to result in uninteresting, low quality comments as the subject matter diverges from the topic at hand, or flamewars, so long-term engagement is discouraged.
No, HN doesn’t have read/unread state, and also cuts off discussions after a day. This makes checking for new comments tedious, and prevents any longer discussions.