[Dead] means they've been downvoted to oblivion. Moderators had nothing to do with it -- those were other users on HN. I always browse with "showdead" on and the vast majority of [Dead] posts are awful. They don't need to violate HN Guidelines, they were killed by the community.
[Flagged] means it was killed by a moderator. Those are more rare. I don't agree with everything that is flagged but I think HN has a great moderation policy overall. Often when posts are flagged, the moderator responds explaining why.
Flagged 100% does not need moderator involvement. Even being post restricted needs no moderator involvement.
I have had no shortage of comments flagged by a certain group of people that like their “alternate facts” and share their HN posts to discord for brigading / mass down voting anyone that calls their lies out.
It only takes 2-3 quick user flags for your comment to be permanently, automatically flagged, and only a couple of those to get comment restricted.
Comments cannot be hidden by downvoting. Comments are marked [flagged] [dead] only after other users have clicked on the timestamp and selected "flag." I think that these things get conflated because comments that tend to attract heavy downvotes also attract flagging. The [flagged] [dead] comments are mostly (entirely?) killed by the actions of ordinary users, not moderators.
Comments that are marked [dead] without the [flagged] indicator are because the user that posted the comment has been banned. For green (new) accounts this can be due to automatic filters that threw up false positives for new accounts. For old accounts this shows that the account has been banned by moderators. Users who have been banned can email [email protected] pledging to follow the rules in the future and they'll be granted another chance. Even if a user remains banned, you can unhide a good [dead] comment by clicking on its timestamp and clicking "vouch."
[Flagged] means it was killed by a moderator. Those are more rare. I don't agree with everything that is flagged but I think HN has a great moderation policy overall. Often when posts are flagged, the moderator responds explaining why.