Dropping by to mention and ask a few things :
1.Regarding the weird naming for the 2nd port. The problem is that the VMware ESX device naming mechanism is not handling nicely the fact that the Mellanox device has a single PCIE function for both ports. This results with ESX using a specific calculation for ports other than the first port. The calculation is the sum of: 1000000 + (PCI index * 100) + (port number). From my experience uou can ask vmware for a patch to fix the naming convention algorithm however I'm not totally sure it will still stick with standard vmnicX.
2.Regarding the missing port, as mention in this thread, let us know the FW burned on this card, by the way, have you tried playing with the port protocol change ? for example "esxcli system module parameters set -m mlx4_core -p port_type_array=2,2"