A better question is: does a universe in which there is nothing (and never has been) still contain space? (Though a better question, I wrecked it by introducing "never", which presupposes that the universe has time---even though it contains nothing, and therefore no events take place.)
The question creates a bias because when we imagine matter being removed from the universe, we firstly imagine the removal as an event unfolding in time. Secondly, we continue to imagine the locations where pieces of matter used to be, and those locations continue to be separated by the abstract space which we continue to imagine.