"The space between the planets and the stars is not empty in any sense of the word, even if all the gas particles and protons and electrons that are in the said volume were taken away, there still would be all the photons of light coming from the countless star systems. (photons are something after all.)"

Take away all the photons and there is still Neutrinos:

"Neutrinos are elementary particles that travel close to the speed of light, lack an electric charge, are able to pass through ordinary matter almost undisturbed and are thus extremely difficult to detect. Neutrinos have a minuscule, but nonzero mass.
...
Most neutrinos passing through the Earth emanate from the sun, and more than 50 trillion solar electron neutrinos pass through the human body every second."

http://en.wikipedia.org/wiki/Neutrino

So, a cardboard box could block photons.

But if you made a superduper box out of exotic material.
Say, 100 meter cube box with 10 meter thick platinum walls, put this 100 light years from any star, brought the box to near absolute zero. And using gravity, magnetism, and/or lasers to push out any remaining matter within it.

Then, you would still have Neutrinos and probably other stuff in the box.

Now comparing our platinum box which is a nearly a perfect vacuum with a 100 meter cube cardboard box which has 1 atm of earth's atmosphere, there is somewhere around 99.999 and some amount of .9's after this, less matter in it.
So how how much difference would it make in terms of speed of light if photons are traveling through massive amounts of atoms compared to zero amount?

"The air we breathe has only a trifling billion-trillion atoms per cubic inch. Space between atoms are much greater than the size of the atoms themselves, so air reduces light speed by just a few hundred miles per second - not enough to notice under most circumstances. "
http://www.pbs.org/wgbh/nova/diamond/sparkle.html

In other words reducing the amount atoms per cubic inch by an order of a trillion is probably going make much more difference than reducing it by a order of hundred.