Depends on the emergency. If the courts are open, the public has recourse to them. Civil War case, Ex parte Milligan, 71 U.S. 2 (1866) is the starting place.
It is an open question whether or not a US citizen enemy combatant taken in the US can be kept out of the civil court system, but the likely answer to that is "they cannot."
I think it depends on who you ask, and the conditions on the day you ask it. You're probably right, under the current situation of apparent order, at least on the surface.