So far the Port Royale and Patrician games followed a simple logic: the biggest ship with the most weapons will win a battle. With Port Royale 3 shoals have been introduced – they slow down ships unequally.
Ships with draft 0 can pass shoals without any negative effect. Bigger ships have a draft of 1 or even 2, the later ones will get slowed down the most.
Taking a look at the ship statistics, you will see, that the Military Corvette is the biggest/best armed vessel with a draft of 0.
You can make use of that:
Naval battles against vessels with a high draft should get fought near the coastline. The AI does not avoid shoals, you can use this for you own advantage.
On the contrary, if you have a Ship of the Line with a high maximum speed and 50 cannons, you should only fight far off the coastline. This way you do not have to maneuver around shoals, just sail with the wind and no other ship will catch up with you.