The WAN port is just another port on your device -- all of them are connected to the hardware switch and then they are segmented by means of the VLANs.
Presumably, having one network on eth0 and the other on eth1 should provide the maximum performance (as compared to them both being on the same ethX port), but that depends on the hardware design of your router.
Your routing performance depends mostly on the CPU's capabilities, but also may be impacted by things like software or hardware flow offloading - if applicable and supported on your router.
But, there is really no difference using the WAN port vs the LAN ports in terms of performance in this router.
