I thought those issues were fixed as part of
Bug 20931 - Groupwise Appointments not visible in Web Client after Migration (related to 20278)
Can you still reproduce disappearing calendar subfolders under 5.0?
bdial: Depends what use is going to be made of those shared calendars. Unless they are mostly empty, I can't imagine that a page with "dozens" of calendars overlaid is going to be very usable. Consider not making mountpoints at all. Instead, create hyperlinks to the (read-only) HTML view of the HR calendars on a publicly shared wiki page.
We're going to be doing something like that with conference room resources. Everyone needs access to check the calendar, but nobody is ever going to want to overlay it on their personal calendar.