Link had had some bad experiences with ships in the past. As a result, he'd gained a healthy distrust of pirates, sailors in general, and sea-faring vessels. "I live on a ship with you? Huh. No one lives in trees anymore." Sensible people lived in trees.
Link looked at Ed's hand for a moment before taking it. He could probably trust her. For one thing, she would have been the worst pirate imaginable. But why would Epona be on a ship? Epona hates the water.