Was it right to question german-americans when the united states was at war with their native country?

Sure they have the right to ask them questions, despite the fact that it's not likely that they'd actually know anything about it. However, the German-Americans should also have had the right to not answer and not be thrown in jail or whatnot for it.

 YES, 

they do have  the right to ask them questions. 

People automatically think of the Middle East because most Muslims are in the Middle East since the Islam religion originated there.