They are not. They simply disappear. I have modified the plugin a bit to log any DB deletes and nothing other than manual removals are showing up. The strangest thing is that users always disappear from newest to oldest and that even if they are removed from the MailPoet list of users, they still appear in the WordPress users table.
Tom,
This is truly an example where a bug becomes an undocumented feature. I totally understand not wanting to break it for users that actually like/need this capability. I look forward to your update with the option to turn of the theme sharing.
Kind regards,
John