So, if we use 2008 or later Mulitprotocol, what are the restrictions? Would we still be able to create VHDs? And would those VHDs would give optimum performance? What is the difference between both the protocols?
The LUN types now mostly relate to pre-padding to prevent misaligned IO.
The page you have found refers preventing that for VMs running inside VHDs - not the LUNs that are formatted as NTFS and used to store the VHDs themselves. The GPT restriction is for the guest VMs running Win2K or Win2K3, not the main datastores themselves.
If you are using iSCSI or FC from a NetApp system to a Windows Server to store VHDs, use the Hyper-V LUN type.
However, we also support using SMB3 for shares that store VHDs - which can enable easy access to NetApp Snapshots. Further, if you're just creating VMs to create fileshares on, you can always just connect your clients directly to the NetApp via SMB also.