I've been trying to get my head around how this works, and I think I've got it now. Here's my best guess on what's going on ...

Plugins and themes are backed up just as as they normally would. However the plugins and themes activated for each site are NOT backed up, as are the posts, comments etc. So basically what you need is a single VaultPress subscription for the main network site (as Andrea suggested) and then use a standard backup system (I think BackupBuddy can do this now) to handle backing up the databases and uploads folders for each individual site.

VaultPress will presumably need to do a full security scan through the entire install, so having a subscription for each individual site in a network isn't really necessary since you get the primary benefit of VaultPress (security scanning) automatically with that single subscription.

Now that I've typed this out, I think it's the same thing Andrea was getting at over on WPMuTutorials.com ... http://wpmututorials.com/news/vaultpress-now-for-multisite/\