We deduce that space exists from our senses. Our lifes revolve about things happening in 3-d space and evolving in time.
We consider empty space as space without atoms or other particles. Even if in practice all space has some radiation flowing through and some particles zipping by, we could say that some regions of space are almost empty, at least compared to the atmostphere. We can focus on those properties of space that don't relate to electromagnetic radiation or the few particles we might find. We can call this "empty space".
In classical physics, we talk about friction-less surfaces. You may say: how do we know that friction-less surfaces exist?. Well, we can find tricky ways to reduce friction to negligible levels, but even if we couldn't, we can always imagine a friction-less surface and then focus on all other forces except friction. Abstraction is a very important tool in physics.
Now, if you read that in empty space there are quantum fluctuations and virtual particles and then you say that in that case empty space is not empty, you may be right. But it appears people by convention have decided to call that space empty, and it would be useless to argue.
We consider space as that thing (empty or not) that separates bodies. I guess it would be a valid question to ask if space would exist if there were no bodies, no matter. Probably space only exists if there are some massive bodies floating around, but I would leave that discussion to those who have enough knowledge to give informed opinions (I don't know enough).
The holographic universe is a very speculative theory and I would stay away from it. If I were you I would also not try to understand too much about string theory and quantum gravity as these are very advanced theories that are still in evolution and that require very advanced math. I would stick to understanding quantum mechanics and also the special theory of relativity.
About you comment on what you read about empty space containing more energy than the rest of the universe, if some sicentists think that way it is because they calculated it based on certain assumptions. Scientists normally don't make wild guesses or exagerate. They may be wrong, but because they made the wrong assumptions, not because they exagerated. The assumptions are ultimatelly tested by comparing their consequences with experiment or measurements of the universe.
--Alex--
