I think maybe you misunderstand how Amethyst's feature works.

If a user has been reported (not muted) by 5 or more npubs THAT YOU FOLLOW, their posts will be hidden FOR YOU, using a warning message showing the pfps of the people you follow who have reported them, and giving you the opportunity to show the hidden message.

So, say you are a new user who has not followed anyone. This means that no-one's posts will be "shadowbanned" for you, because you don't yet have 5 people you are following, let alone who all happened to have reported the same npub. Once you have started following some people there is more and more likelihood that at least 5 of them will have reported some of the same npubs. And yes, this gives popular npubs an outsized ability to coordinate so that the posts from npubs they don't like are hidden from their followers.

This is not the same as being "shadowbanned on Nostr" though. It ONLY affects THEIR followers. Anyone who doesn't follow those popular npubs doesn't have posts hidden from them using this method. Anyone who doesn't use Amethyst doesn't have any posts hidden from them using this method. Anyone can choose to show the hidden message by simply tapping "Show Anyway." Anyone can disable the filtering entirely, if they don't find it useful.

I would wager that most users leave it on, though, because it is incredibly useful. The people who I see complaining about it are typically those who have been reported and muted a lot (by 90+ users, for instance), not just by popular accounts, but by a wide swath of users who don't want to see their content at all.