I'd say asking is your best bet.
Ask them if any of there ancestors were ever nuked?
What difference does it make?
I usually see the difference in the eyes and forehead. Japanese guys generally have a bigger, rounder forehead and an even more invisible crease over the eyes.
Is it so important for you to know his nationality? Why? You will treat him in different ways depending on his nationality?
Beside the obvious way (ask him), you can simply pay attention to the way he pronounces R and L.
By his dialect?
Maybe he is Korean.