Clinker planking made it difficult to cut portholes for cannon so they went with Carvel-built ships with an internal skeleton

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Sailing ship tactics from wikipedia

 

 Since these guns were much heavier than the earlier anti-personnel weapons, they had to be placed lower in the ships, and fire from gunports, to avoid ships becoming unstable. In Northern Europe the technique of building ships with clinker planking made it difficult to cut ports in the hull; clinker-built (or clench-built) ships had much of their structural strength in the outer hull. The solution was the gradual adoption of carvel-built ships that relied on an internal skeleton structure to bear the weight of the ship.^[2] The development of propulsion during the 15th century from single-masted, square-rigged cogs to three-masted carracks with a mix of square and lateen sails made ships nimbler and easier to manoeuvre.^[3]