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They're only hidden in the vSphere UI under the Host/Client view, if you navigate to VM/Templates View, you should find vCLS folder that contains all the VMs. They're also not hidden from vSphere API (which includes PowerCLI, which is just another Client to API)
I've upgraded my env several times and its running latest 7.0 Update 2a and I'm able to see the VMs both from UI/API
Get-vm | where {$_.name -match "vCLS"}
Name PowerState Num CPUs MemoryGB
---- ---------- -------- --------
vCLS (36) PoweredOn 1 0.125
vCLS (39) PoweredOn 1 0.125
vCLS (32) PoweredOn 1 0.125
vCLS (24) PoweredOn 1 0.125
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