1. The Sign In page must still be accessible or even admins could get locked out when a site is closed, we don't know who is an admin until they login and the site is only closed to the public. Some people use that feature while the build their initial content before launching the site and may need to login and logout many times.
However it should be noted that really any or all pages could be broken during upgrade including the closed page. As mentioned on this thread it should work ok for most upgrades but there are upgrade scenarios where even that page can break such as when there are schema changes to mp_Sites table which makes it impossible to even check if the site is closed until the upgrade script finishes.
2. I'll ponder that, maybe I'll make a separate page the includes only the checkbox and the edit message.