I can comment on the "Books that Aaron Swartz read, loved and hated" story. OP posted that link to HN and it made the front page. The story was soon flagged by the community (people viewed it as Amazon affiliate spam) and it fell off the rankings. When the moderator dang noticed that the story had been flagged, he decided to restore it (
https://news.ycombinator.com/item?id=13840869). So yeah, that explains why this particular story fell off the front page quickly but does not have any [flagged] or [dupe] tags attached now.
I've learned that it's best not to jump to conclusions based on what you think is true (however sound your analysis might be). Always ask the other side(s) for an explanation. In this case, you could have sent an email to the mods asking for an explanation. If you find their response unsatisfactory, go ahead and write a post explaining why.