Another interested party checking in here - it would seem to me that this is entirely what Cohorts *should* enable you to do, but they don't... You can have those top level categories hidden, and enrol the users into the courses by cohort membership, but this means that the users just see a list of courses they're enrolled on, and no structure (i.e. no hierarchy of categories) to hold those courses. Over about 5 courses, that flat list is useless IMO... particularly when you might have a cohort who have access to a specialised set of 4 or 5 courses as well as the remaining 30-odd that everyone else has.
General help
Hiding Course Categories for Certain Cohorts
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