I found the same thing. We have a four node cluster and 3 out of the 4 machines are upgraded to Proxmox 3.0. I was seeing the same thing, snapshotting was not available on VMs that are in QCOW2 format. I finally realized though that I was looking at the cluster through the one Proxmox 2.3 node that hasn't yet been upgraded...when I opened up the GUI from one of the nodes that is already upgraded to 3.0 the snapshotting is available for those VMs that are in QCOW2 format. Is this possibly what happened here? I just thought I'd mention this in case it helps to possibly understand what may have happened.
Awesome job Proxmox team for an excellent product!
Regards,
ctcknows