I think they can be justified under select circumstances.

For instance, I think a shadowban is justified for accounts that exist merely to post spam or purposely derail every thread, and obviously aren't being used by a reasonable person. If an account represents a long-term existential threat to the quality of the community, then almost any legal means are justified to take action against it. Whether it's a bot or a human who just wants to watch the community burn, let them shout into the ether.

On the other hand, shadowbans against people who accidentally break the rules a couple times, or call someone a doodiehead, or have the wrong politics, or are subscribed to the wrong communities, are largely unethical. It's a form of disembodiment being imposed on an individual who has a reason for wanting to communicate with others, even if their communication is considered disagreeable.

Sadly, the latter is far more common on Reddit.