I'm not sure how hard it would be to make the display catagory based. As it is, threads is not catagory based either. If the user does not have the correct group access for the boards under a catagory the boards are not displayed. Neither is the catagory since there are no boards in it to be displayed.
If you limit users to specific boards then the information displayed on the index page will only be from them boards. (with exceptions to information such as Top X Posters or Short Stats as this information is not based on board/group access. (probably a couple more boxes not coming to mind)
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