The phrase "Happy as a clam" makes a little more sense when you hear the full expression: "happy as a clam at high tide." The clam is supposed to be happy at high tide because it is safe then from land animals and people digging for it (but come low tide, watch out!) This idiom is supposed to date from American colonial times.

Sources:
http://www.bartleby.com/81/7945.html
http://www.erickraft.com/markdorset/topicalguide/happyasaclam.html
http://nersp.nerdc.ufl.edu/~nickym/Cliches.html

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