No, they wouldn’t.
They would exist outside of our universe (since they created the universe), so the rules of physics in our universe don’t apply to them.
Even if the reality they existed in had something equivalent to atoms, it would be inaccurate to call those “atoms” since they are in different realities.
Why are you pretending that is some sort of gotcha?
Diplomats communicating with their nation’s allies does not make them legitimate military targets.