For more sophisticated management of a large cluster, the best option is probably to use Powershell, potentially in concert with some orchestration, to automate the creation and maintenance of jobs. It should be fairly easy to create a Powershell that list VMs for each CSV and adds them to a job, although I'll have to admit I've only done this for VMware. I would guess the first step would be to grab a list VM objects with Get-VM, then the list of CSV objects with Get-ClusterSharedVolume. At that point simply looping through the CSV objects to determine which VMs live on them should be a simple matter of comparing field (I think the VMCPath property of the VM object would be matched against the FriendlyVolumeName property of the CSV object).
So once you have the list of VM objects it should be pretty easy to create the job and/or add VMs to an existing job. If you use some orachstration you can even trigger a script to add a VM to the appropriate job automatically as soon as the VM is created, otherwise a simple scheduled run of the script each day would pick up new objects and create new jobs.
That's the conceptual idea anyway. I've seen this done for plenty of environments with VMware so I don't think it would be too difficult with Hyper-V, but I'll admit that's a platform I'm still ramping up my knowledge on.