Concerning high wind and sea: I've heard that sailships rather reduce their sails in storm conditions. I've also heard that ships would rather sail around or stay in port, the smaller - the more likely they are adversely affected by heavy weather. So I don't think heavy ships go faster in heavier weather - it's rather who can go through heavier weather at all. And in really heavy weather I don't think any ship of that time would be able to make any use of its weapons with all the rolling, waves and poor visibility - again - the smaller the ship - the more adversely affected it is in heavy weather.
Of course you'd need to simplify for game mechanics and if the game mechanics don't represent reality that's fine too. The important thing is that they make things fun and balance stuff while still maintaining the spirit of the game.