The meaning of update.php pending updates
It's part of menu_update_7003(). The comments in that function say it all really:

Make sure all custom menus are present in the active menus variable so that their items may appear in the active trail.

Usually just searching Google for the exact message in quotes (e.g. "Add missing custom menus to active menus list") will bring up the page that explains why it's been done (that's what I did to find this out). You can most likely do the same for the other two updates and find out exactly what they're doing.