Most ski boats have double bottoms, ie the area where the foam or bottles are placed.
Most boats would actually float with their double bottom flooded, however much deeper in the water, and in flat water could be ok....less so in waves.
Id be surprised if your double bottom is one compartment such that you could loose all your bottles through one hole.
Also unless rolling like a behatch....the bottles own buoyancy would push them up, and not down through the hole......you could start loosing bottles, but I doubt it would be a mass exodus.
I have foam, but would prefer bottles, but then I am Cat R, so expect flattish water. My boat can float with the entire double bottom flooded......so actually would (in Cat R) have preferred nothing in the double bottom, and would have left its watertight integrity in tact, instead of making holes and fitting hatches.....and having foam that can absorb water and weight