"Hull of a problem" sounds like "hell of a problem" which is a saying meaning that something is causing a big problem. The hull of a ship is the main body of a ship, it includes the bottom, sides and deck of the ship. The hole at the bottom of a ship was a problem occuring in the hull of the ship. It was a "hull of a problem" literally. The joke is playing on the word "hull" and how it sounds like "hell" and how it's used to fit the saying "hell of a problem". 
When the bottom of a cargo ship got a hole , it had one hull of a problem .