HN flagging is just shadow moderation.

I asked dang if I was shadowbanned from flagging. He said yes, if I flag something then it doesn't count because I flagged the wrong things in the past.

The conclusion is that flagging isn't really up to user choice, but is up to dang who decides which things should be flagged and which shouldn't. It's a bit like how on Reddit, the only comments you can see are the ones that agree with the moderators of that subreddit.