I'd think about it completely differently than a boat.

It's true that sailing would be impossible since it's been pointed out that sailing relies on the resistance of the hull in the water to navigate effectively. But that's not true for aviating like you might do in a balloon, which is essentially what you have. You have a flying craft that simply flies very close to the ground.

You haven't specified how far above the surface the craft would hover, but I'm assuming that it's at least a meter (~3ft) so that it can get over most of the mundane waves and swells. Your technology level doesn't really allow for using fans like a zeppelin or blimp would use to steer, but you could still navigate just like a hot-air balloonist would.

Like the Polynesians, your civilization would be familiar with ocean and wind currents, but with a bias towards the wind aspect as that's the strongest form of propulsion. Knowledge of the currents would mostly only be useful for tracking prey.

As far as the design of the craft, I can't keep from thinking about basically an upside-down boat or canoe with some sails coming off the top. It could be mostly crested or rounded along the top all down the length, getting wider as it goes down into a large flat base for the repelling material. You can use sails or even kites or parachutes to grab the wind, and wings or tails like on airplanes to steer. Remember, you're in the air, not on the water.

As other answers suggest, the wider base will provide stability but since you have basically a sink proof material it won't really matter if the craft was totally swallowed by a wave. As long as the bottom was wide and heavier than the top, the craft could easily rise back up from underwater. Maybe some kind of air bladder/attic sealed with tar at the top could help keep the thing upright.

I'd think about it completely differently than a boat.

It's true that sailing would be impossible since it's been pointed out that sailing relies on the resistance of the hull in the water to navigate effectively. But that's not true for aviating like you might do in a balloon, which is essentially what you have. You have a flying craft that simply flies very close to the ground.

You haven't specified how far above the surface the craft would hover, but I'm assuming that it's at least a meter (~3ft) so that it can get over most of the mundane waves and swells. Your technology level doesn't really allow for using fans like a zeppelin or blimp would use to steer, but you could still navigate just like a hot-air balloonist or glider pilot would.

Like the Polynesians, your civilization would be familiar with ocean and wind currents, but with a bias towards the wind aspect as that's the strongest form of propulsion you'll use. Knowledge of the ocean currents would mostly only be useful for tracking prey.

As far as the design of the craft, it should definitely get wider as it goes down into a large flat base for the repelling material. Water would just stream off it down the sides. You can use sails or even kites, balloons or parachutes to grab the wind and pull you along. Control surfaces like wings and tails on airplanes help you steer. Remember, you're in the air not on the water. As long as you can keep your means of moving and navigating intact, your craft should survive just about anything.

As other answers suggest, the wider base will provide stability and since you have basically a sink proof material lining the bottom it won't really matter if the craft is totally swallowed by a wave. As long as the bottom is heavier than the top, the craft will rise back up from underwater. Maybe some kind of air bladder/attic area(s) sealed into the upper/highest parts of the ship. As long as your decks drained you could temporarily be fully submerged and probably come out ok.