@gaigous It's entirely possible, likely even, that with how rare flying ships are in this world, it originally belonged to a noble (because who else would have the coin for that kind of thing) who used it as a pleasure vessel only for it to jacked by pirates (at least, I think that's what they were, it's been too long since the last chapter), who then outfitted it with cannons; such a story wasn't all that uncommon during the Age of Sail in our own history, so that could be the story here and why a good sized armed vessel without the means to defend against its own arms exists.
Alternatively, think of it like a game of baseball: the average fastball speed of a major league player is about 90mph. Coming off the bat, the ball's speed can increase to 110mph or greater depending on the force from the batter. Even if you're wearing a helmet, both would kill you if they struck you in the head, but one's going to do a
lot more damage. Now scale it up to, say, a 10lb round shot going about 230mph that gets batted back by a superhuman capable of wielding a magical log strong enough to not shatter under the force of the shot and you could probably go so far as to double the return speed; when combating armor, speed wins every time.