My point is you don't notice every post that gets removed and there is currently no transparancy on the reason why.

HN doesn't have to be transparent, it's just a site with it's own agenda (by that I don't mean evil agenda, but it is there for a reason) but if you want to grow the community, I think clearly identifying why things were removed is a reasonable thing to ask. If every one it marked "flagged by users" I'd worry that there is no manual intervention.