I’m not sure the judges have the same standing with an NE order as opposed to an EO. Are judges not neutered under a NE? If aliens land on the WH lawn and the president issues a NE order, what judge would have standing to challenge that?
Trump has the authority to issue a National Emergency Order under the National Emergencies Act, which is a law like any other, and spells out what is and is not a "National Emergency."
Interpreting the law is what courts are for. And if you read the statutes, there is a lot more wiggle room for the bad guys to argue that a state of emergency does not exist, than there was for the Travel Ban, and we lost the Travel Ban argument right up until the Supreme Court's 5-4 decision.
So yes, the courts would have standing to block any declaration of National Emergency until the argument of whether a state of National Emergency existed was fully played out in the courts.