I think they parked in deep water on purpose, because the ship would be hidden better there. Cora, Hook and Regina knew of the other spot. Though they left Hook tied up, he has a way of getting out of those situations. Though that makes me wonder, how much angrier is he going to be when he realizes they jacked his ride!
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“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass