Hmm... Well this is interesting. I will say that Faith did play a major role in the 18th Century. However I will say that there needs to be a very distinct line between Faith and Morale. It is fine to have faith, everyone has faith. If you don't then when you say I believe in X, (X being the condition of what ever the hell you want) then you have faith because faith is the ability to have full belief in a subjective certainty. Morale is the ability to have heighten spirit in what you believe in. Anyway that was that tangent.
To the original topic, ought it be a part of Naval Action? Well if this is suppose to be a realistic feeling game in the 18th century I have no issues with having religion in the game, though does it need to be part of a major role in a player controlled community (META TALK ABOUT OPEN WORLD)? No I think that it is redundant and would cause flame wars with in the game. I would say that the nationality of said player is significant enough that religion can be left out of the equation. One can argue that religion did play a major role and should be incorporated in the game though here is the catch, although naval action, when it is open world, want to embody the 18th century experience, and players must choice either the big three (Theist, Agnostic, Atheism) it would cause unnecessary tension in the player community where there will be flame wars about god existence or why you believe. Just having the entitlement of being in/apart of said nation of an individuals choice should be enough to adequately suite the role playing experience.