WordPress Multisite shows the "WP-Super-Cache" item 2x in the left menu. It's displayed under both Tools and Settings.
Here is a screenshot: http://img191.imageshack.us/img191/4939/y34y.png (MP6 / other plugins have no influence on this).
There was a similar post 2 years ago: http://wordpress.org/support/topic/delete-cache-and-list-files-on-multi-site
Could it be listed just once on the network sites? I believe that individual site users should have access just to the Clear Cache button so they can't change any settings. Anyway, nothing major :)