It discourages reflexive replies. The depth limit is a soft one, just an extra step that perhaps gives one a chance to pause and cool down.

This baffles me so much. It would be so simple and valuable to add.

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.

All these decisions add up to people just not replying to interesting questions.

More often than not, nobody will reply, so all threads are just one or two levels deep. Or in the rare case someone actually replies to an interesting point, it's usually not the original poster. Probably because they had no idea that anyone had even followed up on their post.

Requests for elaboration mostly go unanswered, and comments are made expecting no replies. So people just shoot ideas into the void, with interesting interactions only happening when someone famous comments.

I think the main reason for flame wars isn't the depth of threads but the users. Usenet had no such depth limits, LessWrong doesn't have them today.