I like the idea of making shooting in the rain, fog, snow etc more challenging, but may I suggest another idea along the same lines you were just describing, but a little different. Instead of decreasing the accuracy of muskets via numerically changing what I'll call the "accuracy modifier" in the game's code while raining. Why not decrease the players ability to see clearly in the distance? I don't know the correct terminology for it, but rain drops, snow flakes, and fog absorb / refract light, making it harder to see things clearly in the distance. I personally feel like it will be hard enough to consistently hit targets at range anyway, because of the variation of smooth bore muskets (which probably will be written in the code), not to mention the new ballistics system.
I do like the idea of having a chance to miss-fire in rain, and in small boats where spray is likely, but I do think if that were to be a feature, that admins should have the ability to turn it off on private servers. If we are going to have competitive leagues, I don't think many regiments will favor this feature being mandatory.