Yes, mutt should be able to shutdown nicely. When editing a draft email though the external editor, e.g. vim, emacs etc, also needs to do something sane.
For starters, the temp files of any draft you are editing can be saved in a custom tmp dir, e.g.: set tmpdir = "~/Mail/mutt-editor-drafts/" This is often better in an emergency than having /tmp/ cleaned on reboot and losing your draft. Downside is you must manually check and clean that directory now and then. If mutt were to process a unix "shutdown" signal, it could (assuming concurrency issues are carefully thought about and handled) save current mailbox status changes (like stuff "^q" or save-mailbox etc). This sounds like a relatively "easy hack" (as the libreoffice guys call it) for someone new chomping at the bit to start learning mutt's code :)