The Nazis might have been evil but at least they were "like us" in that they shared a common heritage, religion and linguistic root with Americans. Japan, meanwhile, was portrayed in American propaganda as an inscrutable hivemind run by a primitive death-cult.
You can see the same strange mistrust of non-Christian culture applied to Muslims in America today - even though the vast majority in the world are not violent terrorists, many Americans suspect that Islam taints and "radicalizes" the mind with evil in a way that Christianity doesn't.
Even in modern Japan itself ironically enough, it's hard for some people to really picture non-white and non-african Americans as Americans. The word 外国人 (gaikokujin) really only applies to foreigners of European and African ancestry. I believe it's hard for them to picture those Americans as Americans simply because of the image that has been painted of the country.
Sincerely, A non-asian non-african non-white American interested in Japanese culture
I believe it was both - they're two sides of the same coin. Look at the propaganda of the time - the Japanese were portrayed as being fundamentally inhuman in a way that Europeans weren't. The myth of the "inscrutable Oriental" has been around in the West for a very long time, the Japanese mind and morality were considered to be incomprehensible.
That Japanese Americans looked different probably made this xenophobia easier to act upon, though.
Christianity and whiteness are surely connected in the cultural consciousness.
Also, Germans had been immigrating into the US since the year 1700 and intermarried widely with other groups. So it would be very hard to decide where to draw a line and say someone is "sufficiently German" to be interned.