It's probably some sort of science we don't even remotely understand. What I've seen is that the "gas" inside the morph ball has some form of solidity. Maybe Samus is converted into some sort of gas so she can fit in the ball. But such a drastic transformation is very dangerous and must be absolutely precise or else your whole cellular makeup can be messed up, and such mess ups are.... Shall we say, messy. The space pirates have tried reverse engineering the morph ball technology, and they've failed at every turn.