The clustered hypervisor would protect against node failure by transferring the VM to another running node, but it would not protect against software failure from within the VM. If, for some reason, a CARP'd pfSense instance were to freeze/fail, in this scenario the failover CARP pfSense node should take over. Frankly, I'm not sure which is the more likely scenario: a failing hypervisor node or a failing pfsense instance.
In my particular configuration, I'm not clustering my Hyper-V nodes but instead as stand-alone nodes.