The latest dev version of Superfish seems to solve some of these issues, however, it is generally not recommended to use dev versions in production sites, as these could contain unstable code and could break future updates. Therefore, we are not bundling yet the dev version of Superfish, into our theme distribution.
Workaround - Enabled/disabled state of root level menu itemsThe enabled / disabled checkbox for the first level menu items does not affect their visibility, which is a bug. But it works for second level menu items and beyond. So, to disable menu items one simply needs to make them second-level items, first.
To disable, then, first level menu items, please move these items (and all their children) under another first level menu item, as it seems, to make the checkbox work, then disable them.
This issue seems to be fixed in the current dev version of Superfish, so it should be fixed in the next update of Journal8 as well.