For ships to block trade routes, enemy ships would have to occupy a "wall" around all of your ports that could be used for trade OR your trading partner's ports. The "wall" is what would be needed so that you could not move a ship out of your city with the harbor.
Also, like Sir Ralph said, you can "use" the harbors of other civs that you are not at war at, so those would have to be blocked too.
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