This is actually a REALLY great thing to discuss before the release of With Fire and Sword 2. Surely that, when it comes to naval battles, Taleworlds has SOMETHING made at this time, whether or not it be fun to play, or playable at all. Hopefully they take into consideration some of the things mentioned here.
We all know that the Mount & Blade series isn't known for it's attention to every itty bitty detail, so I wouldn't be surprised if they sacrifice something like sails going up/down, or even rudders turning, and to be quite frank, I wouldn't have a problem with it. However, we do know that Taleworlds would be most likely upgrading their engine for WFaS2, but I'm not going to expect a sudden 100% flawless naval battle system to come with it.
As for mods, it would be quite difficult to have naval battles with the current engine, unless they make it quite simple, like having multiple modes of combat. By this, I mean having one combat mode where two or more ships are set up to fire cannons, and in another combat mode, they would board. Casualties would transfer over to the next fight just like they do already.
However, seeing this happen in multiplayer is just unreasonable and unrealistic. A real naval battle in multiplayer with cannons seems impossible at the moment, so it seems we'll just have to wait. I just REALLY hope that Taleworlds can pull off a successful multiplayer mode for WFaS2 so that ships could fight PvP style, and I even more so would like for it to be successful (if Taleworlds can make that work, it surely will be successful). I just hope that soon I will have my own ship and crew, which would be quite fun.