Are you certain that the plugin has been deactivated? If so it would not be possible for any new emails to be sent out.
Try browsing to your WordPress-install via FTP or SSH and remove the directory
/wp-content/plugins/http-404-email-notifier/. Or delete the plugin from the Plugin administration screen.
If you are caching the database somehow then the plugin activation list might not update properly before some time after you've deactivated the plugin.
It is also possible that your email server had several 404 emails left in its queue, and that these emails were queued up while the plugin was still active. Then consult your email server's documentation on how to delete these emails immediately, or simply wait until all of them have been sent.