Yes. God is in every place because He gives it existence and locative power since He gives being, power and operation to the things that fill every place.
Place is only understandable by reference to actual beings; it has no existence on its own.
Note that "empty space" is a theoretical abstraction and does not describe reality. In reality, the actuality of beings is what determines the actual relations of place.
Actual being, not "empty space", must be our ultimate reference point for any model of what the universe in totality is.