The 'cp' command isn't optimized for VMFS partitions, and - as you found out - isn't thin provisioning aware.
To copy the base (thin provisioned) disks use vmkfstools -i <source.vmdk> -d thin <target.vmdk>. Once the virtual disk is copied/cloned, you may want to check whether the new disk's header .vmdk file has the same "CID" (required to maintain the snapshot chain). If that's not the case, use the "cp" command to copy the header .vmdk file from the "old" datastore to the new one again.
André