If you use "he is just being stupid", you mean that he �s only being stupid at the moment.
If you say "he is stupid", you want to express that you think that person is stupid all the time. ;))
Normally, I would go for answer b) though:
Don�t pay attention - he is just being stupid.
If you use "he always asks silly questions", you want to express that he never asks a `normal� question, only stupid ones, and that he does it every day, for example.
If you say "he �s always asking stupid questions", this would mean that he never stops asking questions - which is not really possible, is it? ;) Who asks questions night and day without ever stopping??
So I would always choose answer a) first:
2 - He always asks silly questions.
3 - We went to the zoo although we�ve been there before.
---> You�re right - the first option makes no sense.