Space is not empty. It is known that in order to truly make space empty, a quantum vacuum, a large amount of energy is needed to do so. In other words, to dismantle space in the same way we dismantle or make atoms (nuclear fission and fission) requires similar expenditure of, if not more, energy. While we have no observable experience of space as we do of objects we can infer from the behavior of objects in space to know about space and time. Space seems to be a special kind of object.
But to speculate on this though is futile. We do not need to know everything about an object to understand it. The car is an example. I can drive it without knowing how the engine or steering work. All I need to know is a car will go forward if I step on the accelerator, and that it will turn left if I turn the steering wheel anti-clockwise.