Interesting, I tested by creating a user ‘test’, committed, then tried to delete the user but it doesn’t disappear from the config (like your symptoms). Since /etc/passwd is modified on boot from the saved config, I found that deleting the ‘user XX’ snippet from /config/config.boot, and then rebooting, successfully removed the user from config & from /etc/passwd etc. Note for cleaning up you may need to manually delete /home/test.
I would consider this a bug but not sure if there is legacy reasons why a user is never truly deleted. I’ll email vyos-users for feedback from the devs.