Clover decides that it's too dangerous to trot out on deck in this storm; she could be thrown off the deck, or against something less than cushy. While there would be plenty of ponies around, she doesn't think many of the crew will be able to immediately tend to her in this storm.
The violent swaying of the boat made it harder for Clover to keep her ground. In the living quarters, she had two choices; hiding in the kitchen, or hiding in a hammock. With how much noise she was making, she was doubtful Sabre would just stumble by.