I'm not sure why, it certainly happened quite a bit. The Italians certainly engaged in numerous naval wars. Genoa and Venice fought a total of 4 across the 13th and 14th centuries. The Battle of Meloria was incredibly decisive with respect to dominance of the Tyrhennian. Both the Fatimids and the Mamluks had navies that contended with the Crusaders and others. The later 13th century really represents a period with intensive naval activity, particularly in the Eastern Mediterranean.
There's a rather nice collection of essays that Boydell and Brewer published fairly recently on the subject: https://boydellandbrewer.com/war-at-sea-in-the-middle-ages-and-the-renaissance-hb.html.
War at Sea in the Middle Ages and Renaissance.
Naval battles weren't common and not at all like they are in modern wars. There were naval battles in the Middle Ages but they began later and were much less common.
For instance, it was recorded that Julius Caesar put catapults onto a boat and fired them onto land against the Britons, but firing catapults to other boats at sea would be terribly inaccurate. It wasn't until 1338 during the Hundred Years' War that there is a recorded naval battle using artillery. Being that the first recorded naval battle using artillery was in 1338, and the common ending point of the "Middle Ages" is with the beginning of the 16th Century, which also consequently is seen as the "transition period" into using naval artillery, all post-Middle Ages. You can see why there wouldn't be very many battles to talk about, not many happened in the Middle Ages.
Before naval artillery, in order to have a naval battle, two ships would either have to ram each other at sea, possibly sinking both ships and both crews, or they would have to string ramps and ropes from one boat to enough and initiate ground warfare.
It is described in more depth here by /u/Sidonius: https://www.reddit.com/r/AskHistorians/comments/17fklk/before_the_invention_of_the_cannon_what_was_naval/
Edit: changed a couple words, it is still morning for me