Are you using VXLAN based Network Pools or vCNI pools?
If you are using VXLAN Exclusively (no vCNI pools exist), then I think this is fine+normal+expected.
vCNI is only going to happen when required, which is to have a vCNI network pool existing in vCD and then Prepare the ESXi host. This installs the vCD agent which is required for vCNI to function. If vCNI is not required, then you don't need the agent installed (since vShield handles the VXLAN bits).