Hi,
It's not entirely clear what type of vCNS license you're referring to, whether it's standalone vCNS Standard/Advanced (licensed per VM) or the vCloud Suite (licensed per socket). It sounds like the latter, if you're talking about Management and Compute Clusters in a vCloud setup. With the vCloud Suite, although it's a bundle of multiple products (including vCNS), it's licensed and treated as if it was a single item. So when you assign a license key to the hosts running the Management Cluster (for vCD), you enable vCNS by default anyway.
If you're buying standalone vCNS, you're buying on a per-VM basis and not per host, so you would not factor in the VM's in your Management Cluster.