It makes no sense to create the same VNI multiple times. It's also not allowed by FRR so it must be forbiddne in VyOS, too
LR1.wue3# conf t LR1.wue3(config)# vrf foo LR1.wue3(config-vrf)# vni 100 LR1.wue3(config-vrf)# exit-vrf LR1.wue3(config)# vrf bar LR1.wue3(config-vrf)# vni 100 % Configuration failed. Error type: validation Error description: VNI 100 is already configured as L3-VNI