Yaseen,
I've already done this upgrade and you will not have issues with VXLAN and VCDNI pools. VXLAN will throw an error but I've just disabled it.
VCD 5.1 supports vCenter/ESXi 5.0 so no issues there.
Only caution to messing stuff up is make sure you backup your vCNS (vCloud Networking and Security = vSM now) before the upgrade. Both of my vCNS VM's crapped out during the upgrade. I had to delete them and then restore the DB.
Eric