How odd... wouldn't it make more sense to write the runes on the inside, then, where they're not likely to be disturbed? Or perhaps the ship has some sort of protective coating over them...

Stone is a very peculiar choice of material, too. Besides its tendency to sink, water, especially saltwater will quickly erode it... though perhaps the runes played double duty with that. Granted, magic is quite versatile, so perhaps they mitigated or compensated for many of the drawbacks.