The MetaBaron

With a better damage model that showed how destroyed a part of the ship was, I would be totally fine with removing the armor indicators.

There should be storms that you have to take down some sails to avoid damage, or risk it to run away. Some ships could also have more resistance to taking on water than others (looking at you poor Niagra submarine). I believe this should also completely translate to battles as well.

They are not just glorified rock markers. Anyone that has done any real sailing or navigation in real life knows their primary role is just that, navigation. Through a combination of timing of the light rotation, to its placement and even color in proportion to other lighthouses allows you to accurately determine your location and approach to ports. In a game that does not even give you latitude and longitude lines on the map these navigational aids would be invaluable and fun to use in low visibility situations or even just regular navigation. Before the invention of an accurate clock and thus the ability to find longitude, these navigational aids were very common and necessary. With no light pollution to tell you where land masses were, running aground at night was a common occurrence, lighthouses were common well before the Romans.

Reporting for duty.