The rebuttal makes some good points. However, many are not going to see the contents of flagged comments nor understand the decisions behind them being so. Not to say that flagging isn't justified at times, but scores of posts that are removed with it, are not guilty of the same violation or the posters below the removed comment in violation may not even know what happened.
Agree that the OP should be able to provide a link to the shadowbanned thread (if they're not having trouble doing so), because of course you will be able to see it. The context of how shadowban or ghostban is used, is debatably valid. Because the user can see the thread, but it's no longer obviously available to the public.
As for showdead, seems doubtful that many would have it turned on or even be looking. Once a thread drops out of sight (likely top 100), seems most won't check (even more so if no comments) unless they are searching for something specific (which could be anything).
Possibly a good example of shadowban/ghostban thread, is this recently posted one (below). It also doesn't show as "dead" either, though maybe there is some time element, and can't be seen by the public.
https://news.ycombinator.com/item?id=34838236
(Robot war dogs commanded by soldiers using brain computer interface [video])