Yep -- have done LOTS of SVMotions under ESX 3.5 -- iSCSI, FC, NFS and a mix of all of those. Absolutely no issues (no NPIV in the environment) except for one very large VM that turned out to be active (when I was told it wouldn't be ). It got hung up and I had to putz around at the service console for a while but ultimately got it back (no data loss...just downtime).
In my humble opinion NPIV is more relevant to 'standard' VMotion (ESX host to host) than Storage VMotion (storage to storage).
In former scenario NPIV helps to preserve WWN settings when migrating a VM, because physical HBA WWN on target host will be different from source. From the doc you are refering to: "This will ensure that the NPIV connection is maintained when the VMotion takes place. Otherwise the VM will default back to the physical HBA WWN and will not be using NPIV."
In latter scenario HBA WWN doesn't change as the VM remains on the same host.