For small passages, I agree that swimming is easier; however, for the open sea the ship is MUCH faster. Remember that it, like the Nymph Lake Raft, can "run" by pressing the Run Key (default Shift) while sailing -- this speeds things up tremendously. Also, correct me if I'm wrong, but it seems like you have a greater line of sight when on the boat, making exploring much faster.
I don't think that you can get to the other sea until you complete the Pyramid Temple on the Desert Island.
Oh, and I've had like 30 encounters (spawn set to Often) with crabs and have gotten *TWO* shells. It's probably a random thing, like with spider eggs, but it seems that the Random Gods aren't with me on this one. I wonder if, like the spider eggs, the shells could be "pickpocketed" from the crabs...
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