After I stopped panicking, I figured it out. Still don't know how or why my ship was damaged. The only thing I can think of was that maybe the pirate ships move and one sailed by, saw an unarmed unwomaned ship and decided it needed some damage. Good thing I had plenty of wood and cloth from my tailor and carpenter. It took a ton to get it back to new. I'm thinking that from now on, I will keep my ship closer to a dock somewhere when I logout. I normally just leave it wherever I finshed up fishing for the day.