They're data/energy AND they shrink.
Their state inside a pokeball is a malleable energetic miasma. They can stabilize into a shrunk form when trying to escape a pokeball - hence the shaking - but most of the time they're in an unconscious, energetic state, which is why it's not inhumane to throw your balls around or not take them out for days. And it's why they can be transferred and stored digitally. Their attention can be piqued, like a sleeping person waking to the sound of their name, which is how they can have awareness of a situation and exit their ball if they want.
Their ability to become pure, shapeless energy is the only way their ability to shrink and use supernatural powers is explainable anyway. They don't follow physical logic or the laws of normal reality.