Actually, as a DM, I'd do my best to try and knock at least one of the characters overboard.
The armor check penalties for swimming are there for a reason, and if a player is dumb enough to wear his full plate armor on a sailing ship he deserves a good old trip to the briny deep.
By eliminating the chance that they'll fall overboard, you are avoiding one of the great dangers (and hence one of the biggest interests) in "on-the-open-seas" combat.
Be sure to apply this to enemies as well though...
In a storm tossed, cannon firing ship to ship fight, I'd be really surprised if at least ONE person didn't get wet.
And as long as they have a decent constitution, and are ok with cutting straps on their armor, they should survive.