Any reasonably sized university installation of munin will suffer performance problems. If they can get munin-update to complete it's run in 5 minutes it still takes some I/O to update ~26000 rrd files.
Rrd 1.4 (1.3?) introduces a rrdcache daemon which collects updates in memory until they are needed on disk (at graph time, and munin-limits time). This consolidated the updates to disk. We must optimize to use this properly.
Another consolidation that would be to store all datasieres values from a plugin into one rrd file as detailed in a comment on this ticket.
Guessing this is suitable for 3.0.