>(Sidenote: Ah ok. So that's how to reply on HN once a comment thread has reached a certain depth: click link then reply.)

I don't think it's about depth; you can't reply to very new comments (presumably to give people a chance to delete mistakes?) but if you refresh the page a minute or two later the reply link will be there as normal.

The reply link takes more time to appear as the thread becomes deeper. The purpose is to create a 'cool off' period to avoid very heated discussions.

Ah, good to know. Still, seems silly when you can just click link then type in a reply.