If a topic gets 40 comments before it gets 40 votes, it gets auto-penalized even with no flags. (too controversial)

There are also other mechanisms, such as vote-ring-detection, that can kill a topic as well.

(That is my current understanding anyway, I am not HN staff, and I am not saying whether I agree/disagree with any of these mechanisms, just stating them to help alleviate your confusion about why some topics may be doing very well and then suddenly die -- it's not always because of flagging)