War over technology card says that when I win a war I can steal blue technology cards instead of science points. Is this always true or only when the opponent doesn't have enough points?
It is always true: there is no limitation placed on when Special Technologies can be taken.
What happens if I have the same blue technology of the same level already in play. Can I still steal it from him and throw it away?
I would say no, as a standard rule to TtA is that you can't have two copies of the same exact Technology card (either in play or in your hand).