I have defined new category with Learner Access by Organization (Ex. Human Resources), but another user with different Organization (Ex. IT) can view
this created Category.
Note: I'm on R12.1.2
All of your users will be able to view and click on the Category itself, but if you've enabled Learner Access by checking off the "Restricted" check box for your Classes, Learning Paths, Learning Certifications, Forums, and/or Chats, users will only be able to see / request enrollment in (or subscription to) the items for which they have been granted access. There is no way currently to hide the Categories themselves from Learners / Managers when they browse the Catalog.
I hope this helps!