From how to remove vyatta user - #2 by cgb
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.
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.
This seems this is still true; that the /etc/passwd file is modified on boot. 