To stop sea trade you would have to stop all trade entirely, because as soon as a trader is built and a shipping link exists, trade occurs. The simple way to do this would be to remove goods and traders and assign a decent fixed income to ports.
The, somewhat different, approach I have gone for is to remove all shipping and keep ports, traders and trade goods intact. This stops the ridiculous "high speed" movement of army stacks all over the map and eliminates overseas trade altogether. Instead of sea trade you exploit the "local trade" income as a means of generating income per province based on the goods present. You would have to increase the value of the goods somewhat to make them worthwhile and perhaps add more goods, especially to landlocked provinces, to balance it out. The "local trade income" will then generate florins based on the goods and level of the trader built. Ports are retained and agents can still move from port to port.
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