Hello Deemy,
I always prefer following:
a) Offline /switch the service groups if you want to shutdown one/some of nodes of cluster
Above step gives you much granular control over the situation. When you mention that you have VVR, is VVR configured in VCS as Global Cluster ?
Also, is it VCS or VCS One as 2.0 seems to be pretty old for VCS...
In case you directly shutdown/reboot the boxes, impacts might be different, VCS would take it as failure & will evacuate service groups to other nodes depending on the policies you have set.... In case of reboot, it might be harmful if you are using IOFencing since not all the modules will be shutdown gracefully which might leave some stale keys on the disks...
I am not a windows expert, more in unix, but above considerations are very generic to cluster concept..
Gaurav