Don't worry, I agree with you. The lack of a significant number of ship types, as well as the ill-defined "ship of the line" and "man o' war" types, means the +50% bonus shouldn't be used--straight strength scores should work.
I can see a system where hull strength is represented by the overall strength of the ship, and then warships receive +X% against all naval units to reflect the fact that they are better armed for their size. For example, a merchantman and a frigate might have the same strength of 6 in this new system to represent they are similarly sized vessels, but the frigate receives a +X% bonus because it's a warship and has more guns. Pirate ships, which are not as well-equipped as standard navies, would have smaller +X% bonuses. A series of naval-specific promotions could be implemented to enhance this system--we already have veteran crews, extra cargo holds, and better navigation. Taking some inspiration from the Pirates game, we could have a Bronze Cannon upgrade to give 2 first strike chances and Iron Scantlings to increase strength by 1, or something like that. Marine Detachment promotions could be "borrowed" from the Buccaneers mod to give boarding capacity.
Borrowing another idea from Civ, combat bonuses could be given for coastal as well as ocean areas, based on what kind of riggings gave advantages in those waters. Frigates and light ships get an advantage in coastal waters, larger ships of the line in the deep sea areas. Something small, like a 5% or 10% bonus.
My other issue is with the naming of the ships--what are the man o' wars in the game, anyway? First-rates, with 3 gun decks, it appears. It would be nice if colonials could be proper brigs and frigates, and ships of the line would only appear through the king's navy or foreign intervention in the New World. To my knowledge, colonies did not maintain even 3rd rate ships of the line (the famous 72 and 74 gun designs), much less the heavier versions. Also, the option for the English colonies to construct the famous heavy frigates of the early US would be a welcome change.