So I solved the issue before with the course catalogue items not being visible, but why can't the super admin see all of them on the LMS side?
the superadmin sees everything, unless your settings differentiate what different users see...
It doesn't depend on the user level, it depends on what you set for catalogue and its visibility.
From the information you provided, I guess you created a specific catalogue and assigned it to specific users or specific org chart nodes, that include students and instructors but do not include superadmins, that maybe are in a different node.
Am I right?
I suppose I just would not have expected to have to assign superadmins to a course catalogue. I don't have any groups or organization settings specifically configured for superadmins that I am aware of.
There are some other settings affecting the catalogue, check them under the administration settings > elearning