When you have a topic box that you have marked hidden, it correctly marks all the items inside of it hidden as well. We have many users that like to keep files and other items in a hidden topic box, but the activities/files/etc themselves as not hidden. This allows them to link to those in various places throughout the site, and avoid cluttering up the front page for students.
They are still able to go into the 'update' button and in the 'common module' setting flip it to visible and achieve the desired result, but this quite a bit slower then being able to use the icon. It seems like one way or the other this should be standardized.