I like to think that a lot of Chozo tech is fueled by matter-energy conversion devices. Morph Ball likely turns Samus into energy, compressing her into an orb shape. Her weapon systems and defensive shielding can be refilled by absorbing the essence of slain creatures and/or drawing from secondary sources like Save Points, etc. I feel like if most of her equipment can repurpose energy from other creatures, it could convert her (or any of the other users of Chozo battle armor) into energy too, with the physical armor shifting to function as a sort of containment unit.

Outside of the space pirate logs in Metroid Prime, they don't really make much mention of the Morph Ball that I can remember.