Believe it or not, I'm already experimenting with merchant mods.
I discovered a couple things so far relating to your points:
-You can easily extract the ship 3d models and look at them using wings3d or some other tool with .obj file capabilities! It's very intuitive. I also want to add lots of new merchant ship types, and tweak a few existing models. Most of the ship models are excellent; others could be altered a bit (I have blueprints of some of the actual merchants in the game).
-You can also extract the images for different contacts on the 2d map. So it should be possible to create a more difficult map that displays less information about ship type and nationality. And is not an all-seeing omnipotent "radar"
-I still don't know exactly how ships are armed, but I expect to figure it out soon. Probably one of the excel databases. You are right about ship armament. As early as 1940, thousands of British cargo ships were armed. By 1941, nearly all British ships would have been armed. By 1943 ALL British and American ships on oceangoing convoy routes were armed, according to my historical sources. Usually at least one 4-5" gun, and at least four antiaircraft guns of .50cal - 20mm. The only ships that would not have been armed would be small craft that never left the safety of harbor.
-You can adjust spawn probability for the small groups of merchants easily. All part of the excel files. That way, no countless batches of unarmed 3-4 ship groups.
When they finish development and make the SDK available, I imagine modding will really heat up around here.
