Yes Sarah, I know it's anatomically impossible, but that's the entire joke when it comes to Samus and her morph ball form...
...or maybe it's not? See this Youtube video that seriously explores the plausibility of the morph ball. I neither agree or disagree with the video's conclusion - all I know is the guy who made it sure has a lot of time on his hands.
As I was drawing this, I felt my inner art critic scream foul at the sight of Samus, for her ball form is anatomically impossible. It's creepy to see the human body contort so dramatically, to such a degree that you're capable of traversing cramp passageways. But, this is a comic, and as such, these things are possible in the work of fiction.