The actions against a self-declared “nation” which declared that the Constitution did not apply to them are not by definition unconstitutional. The court of that time took no further actions nor did the congress or anyone else take any active actions to force Lincoln to withdraw anything.
He did not allow the confederacy and their SC sympathizers to have it both ways; to ignore the Constitution yet demand it be applied to them.
I guess my point would be that the Presidents do whatever they can “get away with” - to the extent of whether someone can actually stop them or not.