An open-hulled outboard motor boat is not designed like a ship. Ships are designed and operated to have decks awash with no problems, they aren't motor boats with open hulls ready to fill up with water like the motor boat experiment.
If methane eruptions were causing ships to go down, at least one of them would have escaped to tell the story.
As a merchant mariner, I've never heard of such an occurrance.
I've seen swamp gas seeps offshore, and in the swamp. Most of these are decaying plant matter, biogenic methane, not prehistoric natural gas methane.
A cool video showing scientists playing around and lighting off arctic swamp gas pooled under ice:
http://www.youtube.com/watch?v=Wofv9o0j1Ew
Whole ecosystems have developed in the Gulf of Mexico deep water methane fields, complete with brine lakes and communities of life, all independent of the sun's energy: