As the CMS1000 is based on a standard UCS chassis, there should be no issue with the VM's after - just make sure to check and follow any procedure for VM Tools installation. Also be careful, ESXi has option to upgrade and retain data or upgrade and wipe data. You dont want to wipe all your VM's out.
I do not believe 6.0 > 6.5 requires a new license either.
I recently did a similar upgrade on a couple BE7000 servers with most of the collab suite, and all went without any issues once the server was online and VM Tools were all happy.