I've got the same issue with no information in those physical and logical mapping fields for VMs even though the datastore is on an array that Profiler is succesfully monitoring.
From previous queries the recommended number for each poller is around a maximum of 200 VMs but it may be less depending on number of datastores, VMDK's, load on the ESX hosts etc. I seem to start running into problems (timeouts, errors, data not collected) at more like 150 but YMMV.
Make sure that your vCenter account has the "browse datastores" priv. - That was missing for me (not enabled by default for a RO vCenter account). - As soon as I added it I was able to see the mapping of VM's through to the VMFS and physical layers.
Interesting comments about collection issues.. time will tell for me!