That would be the case in peace, the Federal Revenue would have been decreased; but the war showed that the North could raise revenue without the South very easily, in fact, the wealth of the Federal government increased by a very large amount while fighting a war against states it was trying to subdue. After the war though, the shipping industry collasped due to the efforts of the Confederate Navy, taking away all those import tax dollars the North was relying on. The North being resourceful capitalist they found other ways to make money.
But who owned Fort Sumter did not affect the collection of Federal Revenues by any large amount. As was seen in the Port of New Orleans, you just bypass the tax man and sell on the black market.