In a court of law, issues are argued by two sides before a neutral magistrate.
I've seen this same point made in a few other places too. Maybe I'm missing something, and I'm certainly not a lawyer, but I don't think it holds water.
In a trial, the case is argued by two sides. But other things happen in courts besides trials — such as warrant requests. Those don't use the adversarial process AFAIK.
FISA aside: if the police suspect you have stolen property in your house and want to search your house to find it, they go to a judge and explain why they think you have stolen property. If the judge agrees that it's a reasonable suspicion, he or she issues a search warrant. You're not notified of this, and you don't get to come in and defend yourself. Probably the first you hear of it is when the police show up at your door with the warrant in hand. If they arrest you and charge you with a crime, then you get a trial where you can defend yourself against the charges. But for the search, it's the judge's job alone to weigh the evidence against your privacy rights.
The FISA court issues search warrants; no one is on trial there. You don't get to defend yourself in FISA court, but how is it any different from a normal court in that regard?