It wasn't even the Supreme Court... it was Justice Taney alone acting as a circuit court judge in his ruling in ex part Merryman.
The full court never ruled one way or another on the case and even today it is an open question if the exectutive has the power to invoke Article I, Section 9 of the Constitution.
Thank you for correcting my memory on that.
Taney was not the only Supreme Court justice supported the Confederate cause while still in office...
No Tax or Duty shall be laid on Articles exported from any State.
No Preference shall be given by any Regulation of Commerce or Revenue to the Ports of one State over those of another: nor shall Vessels bound to, or from, one State, be obliged to enter, clear, or pay Duties in another.
These two alone could be used to break the economic logjam placed on commerce between the states by local/state codes.