Well that's not an issue. The beam and missile upgrades have always been more like firmware. The arm cannon apparently manufactures the missiles as they are fired like a 3D printer, which begs the question why there's ammo. In Other M she could restock her ammo if she concentrated enough. Alternatively you could assume the missiles and other things are stored in the same space the power suit goes to when she deactivates it.
She forms Missiles by absorbing the particles around her, transforming them into matter.
See? I came come up with bullshit, too.