Two answers:
1) They don’t always survive. Ships are lost every year to heavy seas. [And sometimes it turns out that a particular design or model of ship is particularly vulnerable.](https://en.wikipedia.org/wiki/Liberty_ship)
2) There are centuries of shipbuilding and sailing experience that inform ship design. Combined with modern design tools and materials, and ships can be designed to withstand huge loads from waves (like dynamic loads of up to 50+ atmospheres in severe conditions). [You can read more about how ship design in this paper.](http://shipstructure.org/pdf/2007symp09.pdf) Unfortunately, there aren’t global standards for ships and, as I mentioned, ships do in fact break up all the time.
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