The ship structure is not infinitely rigid, it has some flexibility and can bend up to a point.
When waves pass through/under a ship then different parts of the ship will experience different forces as some parts will be better supported compared to others.
As long as the difference in forces is below the ship structure’s limits the ship will survive.
If the differences become too large the ship will break apart.
In fact some of the anti ship torpedoes work by exploding under the ship and using this force difference to break the ship in half.
http://www.dynamicscience.com.au/tester/solutions1/war/torpedo.htm
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