In terms of it taking longer to backup, do you have the disks configured differently? Does it reside on slower storage? Are you doing a full backup instead of incremental/diff?
The vm-level backups can happen regardless of what is happening on the vC Ops appliance from a service perspective, but you are correct in that it would be wise to avoid the 12am+ timeframe so that you aren't backing up during DT calc. There 'was' a KB out there on it, but with respect to backup of vC Ops, what I just gave you is a summary of what you'll find on the topic.