Alvin,
They wouldn't have fired a missile. They would have used M60 or .50 cal. machine guns, or possibly a Phalanx chain gun. This ship is also armed with a 5"x54 auto loading gun mount.
Using 2 or 3 .50 cal machine guns on a Skiff would severely dampen their day, and you might say it would ruin it completely. Even an M60 would make a mess.
"And what is a "mothership" to a skiff??? A houseboat???"
"Beer Barge"
A fishing trawler.
Ron