Let me address that idea with a simple answer. Hell No. National Security Courts would probably lessen the rights of defendants and be more flexible about allowing the government to use evidence gained in illegal ways such as torture and spying. Once we allow any weakening of the safeguards of our justice system then that weakness will spill over into all of the legal system. It is easy to see an over zealous prosecutor using a national security court for going after radical enviromentalists or ant-war activists or any other group on the fringe of American society.
The only way we can lose to terrorism is if we beat ourselves. Creating another legal system without all the safeguards is a quick way to do that