The courts side against the government in national security cases all the time. See e.g. Ex Parte Endon, Merryman, Hamdi, Hamden, etc. so I'm really not sure what you're trying to say.
The Supreme Court also routinely addresses political questions, see e.g. Brown v. Board of Education, Roe v. Wade, Griswald v. Connecticut etc. The "political question test" is not a tenant of constitutional law, but rather an element of some conservative jurisprudence. Incidentally, one with which I'm intimately familiar, having taken Constitutional Law from Robert George.
The statement that the Supreme Court doesn't decide issues of national security, from a historical perspective, are just not correct. I've been told it's polite to give people a way out in these types of scenarios, but this is Hacker News. I don't disagree with some "unwritten precedent and protocol," I disagree with your statements.
All of which, by the way, I've proven wrong citing specific case law. This isn't discussion sections or precept. You can't not do the reading, wave your hands, and expect me to go along.
You may disagree with this. But, the Supreme Court has a staggering amount of written and unwritten precedent and protocol that is considered. And national security based cases are unlikely to be subject to as strict of scrutiny before the Court.