They dont breathe. I assume they occasionally require air to cool down the ol insides, but breathe? nah. they can walk around freely in space, and stay indefinitely underwater. I dont know bout the bubbles, but im thinking the "breathing" animations are just built into them to make them look more human. I mean, there is NO reason why X or Axl should be able to breathe in Sigma Palace. And yet they do their breathing animations.