There is no such thing as empty space as it is said to be inhabited by dark matter.
Now you're throwing in another concept you don't seem to understand. Dark matter doesn't permeate all of space. It probably exists much like normal matter, clumping due to gravity. Also, one of the defining characteristics of dark matter is that it doesn't interact with photons (thus the name "dark) so it would have no effect on the speed of light other than due to it's gravity.