I'm not afraid! Send me back to the Bermuda Triangle
The Theory: Pockets of methane hydrates are released from the ocean floor and cause the water in that particular area to become less dense. Because of the loss of density, the buoyancy of the ship is affected and it sinks rapidly.
Scientists supposedly confirm that the area of the triangle is high in methane hydrates. I will assume this is true, only because methane gas tends to float above the oil deposits. Indeed the one instance that tends to be reported most often is that of an oil rig sinking supposedly due to methane gas. (This was never confirmed) As it is, I still remain skeptical of this explanation. It seems to me, this theory could easily be proven or disproven using a simple bunsen burner, a toy boat, and bathtub.
I can see the sudden release of methane gas rocking a boat. If the release of gas were large enough, even capsizing a ship. (It would have to be one heck of a gas bubble) But I doubt it would cause a lack of buoyancy.
I agree their is interaction between the ocean and the sea floor, but is the gas bubble theory really any different than tidal waves being caused by underwater earthquakes or volcanic eruptions? Futhermore, wouldn't such a release of gas give some kind of seismic reading? Its hard to imagine that a burp of gas strong enough to sink a ship would not cause a vibration in the Earth's surface.
While skeptical about the methane gas theory, I do not discard it outright because nature does some very strange things. This is at least a natural occurrence and is worth exploring.