In 9.0, for the Physical witness host to run the witness appliance VM or a Bare metal host being used as a witness host, the physical host needs to be tagged for witness license manually before adding it to vCenter inventory. Otherwise, the witness license with license name "VSAN Witness Evaluation Mode" will NOT be assigned to the witness host.
This is also true for upgrades as well from 8.x to 9.0. When converting a witness host back to a regular host you will have to un-tag the witness license from the host.
VMware vSAN 9.0
This is by Design for 9.x releases.
SSH to the physical host to be used as a witness host or the witness appliance VM will reside, and run the below command to tag it for the witness license
"esxcli vsan witness license set --enable true"
To convert the physical host back to a standard host, use the below command to un-tag the witness license
"esxcli vsan witness license set --enable false"
Note: A reboot is not required after running the commands to either tag or un-tag the witness license.
To check the current witness license setting
esxcli vsan witness license get