I think the key words are "should not". For example, emacs-lock sets both kill-emacs-hook and kill-emacs-query-functions. If the user goes to the trouble of exit-locking a buffer, they won't be happy if M-x kill-emacs bypasses the protection.
I think something similar applies to desktop. Setting up a desktop can be time consuming. Best to err in the side of safety.
After all, kill-emacs doesn't even guarantee that it will kill Emacs. Nothing forbids doing
(add-hook 'kill-emacs-hook (lambda () (error ""))