Of course it’d be silly to switch themes or deactivate plugins just so you could do some operation. The reason for the suggestion was to ensure the issue was within wp-cli itself and not due to some other influence. For testing only, not as a reasonable work-around.
When WP initializes, it loads all active theme and plugin code, whether it’s needed or not. If a plugin has hooked into the query process to somehow customize it, it could apply this too broadly and inadvertently affect other processes that it shouldn’t be affecting.
That query is correct for emptying trash. You are able to empty trash from WP admin, right? But not via wp-cli? So the correct query is failing to work from wp-cli only. It apparently never executes, otherwise it would have worked. It seems wp-cli is at least trying to execute it, otherwise you’d not see any failure messages.
My best guess is there’s some kind of breakdown in authentication so WP thinks you’re not authorized to delete. Doesn’t explain why category 1 doesn’t return results since no authentication is normally required for that.
I think you’re going to need someone better versed in the inner workings of wp-cli to help you resolve this. Because I’ve cluttered up this topic with a bunch of replies, it is much less likely to get the attention of anyone else. We normally discourage the re-posting of topics, but it’d be the best way to get the attention of someone more knowledgeable of wp-cli. Go ahead and do so with my blessing. Include everything you’ve done to investigate to avoid re-trodding over the same ground again. I recommend using a different title so it doesn’t look like a duplicate topic.
I’ll leave a note in your account saying I recommended re-posting in case anyone should question it.