I doubt very much that ship-boarding combat means you take over the ship. For one, that would make battles exponentially swing in one players favor, which means the winner of the battle would have the possibility to earn double navy size. That hardly seems fair.
And two, if you count your on board troops as hit points, whatever troops you had left after battle losses would have to be split up between the two boats. For example, with full health you board another ship and you take 6 damage (for understandability, I'm using the current 10hp health model), that would mean that after the battle you then have two ships with only 2hp apiece. I don't think that would play very well.
Chances are that if a raided ship loses all its health, the attackers will burn it and return to their own ship.