Back when I got enough karma to be able to flag submissions, I used it on linkbait submissions, but it never had any effect... and I quickly lost my flagging privilege.
I hope this pattern of finding more authoratative and higher quality sources continues. It can only benefit HN.
Keep in mind that many people have a wrong idea of what's off-topic for HN. For some reason they think HN is only about tech and startups, when that is not true at all. Genuinely interesting posts from off the beaten track are among the most precious things on this site. Flagging those is like stepping on wildflowers. That's one reason why people might lose flagging. Another is just by flagging way too much (e.g. dozens of stories at a time). But I'd have to look at the data to answer in any particular case, and even then might not be able to.