I spoke to VMware support two days ago about this and they told me that if I start with a fresh database then the VMs on my existing ESX 4.1 host will not come across with those EVC features once those are in the new ESXi 5.1 vCenter inventory as stand-alone host servers. I would then be able to vMotion them onto an ESXi 5.1 EVC cluster that's using the Sandy Bridge baseline without any problems. If I used the existing database then this would not be possible and I would have to use one generation behind (i.e. Westmere) EVC baseline in order to vMotion them into the new ESXi 5.1 EVC cluster.
I will vMotion only the VM to the new ESXi 5.1 host which will be still accessing the VMFS-3 datastores that those VMs machine files are stored. Once it's on the new host then I will proceed with doing a Cold Migration to the VMFS-5 datastore and finally use Update Manager to upgrade the VMware Tools & Hardware to version 9. So, for this last part with the VMs I will have some downtime which is fine.