Sometimes it was a brief abberation and many of the user's subsequent posts are acceptable (though often still low quality). More often than not, the user continues to be abusive and break site guidelines.
In the realm of non-shadowbanned dead posts I do see a lot of community penalizing of merely unpopular opinions.
If I had a penny for every worthless in-group signaling comment, worthless reference rebuttal and worthless assumption of bad faith that gets cut slack because it's in favor of the "right things" when adjacent comments on the other side are not I would be very rich.
Edit: I look at unoffensive comments to see why that user was shadow banned and when I see an "out there" comment I go down the rabbit hole to see if that is a characteristic comment or a one-off so I think I get a pretty good spread.
When I find users I think are unfairly shadowbanned I vouch for their posts, try to inform them they are shadowbanned and/or reach out to moderators with an ask to reconsider.
I'm not fully comfortable with this system, but I don't think it's bad in the way you're saying it's bad. I'd encourage everyone who's concerned about moderation on HN to read a few pages of dang's comment history.
These people must not hold any views reddit tries to censor. I make a lot of anti-vaxx comments, and on HN my account has never been shadowbanned. I'm able to say what I want even though it might be downvoted and eventually become hidden.
On any mainstream subreddit there's a 90% chance I'll be banned for life. And 10% chance I'll get a shadowban - and 0% chance if a mod sees an anti-vaxx comment they won't remove it. On reddit you post in a sub mainstream mods don't like, and I get automated messages that I'm banned for /r/pics, /r/news, /r/cats automatically without even interacting with them. The only subreddits I can talk freely are removed, quarantined or don't have enough users for any site-wide mods to notice. Compared to HN it's an authoritarian hellhole over there.