I'm experiencing the same behavior, datastores that are present in vCenter (hosting p VDC's) but are intentionally not used nor present in vCloud generate "vcd low diskspace" email notifications. I have set the "Disk space threshold Yellow" and " Disk space threshold Red" to appropriate values, but I still receive the "vcd low diskspace" email notifications that a datastore is 50% full.
None of the set threshold values reflects 50% as a trigger.
Did you get a solution to this issue ?