Personally I believe each ship looked to its Captain more for Morale, faith etc. and the Captain decided what was the law within Naval rules and regs, it is the Captain who should have the biggest impact on Crew Morale, brave, lucky, flogger, strict, tolerant, Religious and so on would all be bigger factors than having a Chaplain on board, some did some didn't.
Talking Religion is a bit like talking Politics we all have our opinions on it, maybe leave it to the player which type of captain they want to be to rule their ship, superstition, amount of Grog, shore leave, prize money and loose women I am sure played a bigger part in the life of a RN Seaman. (Cannot say for other Navies)