The eye sockets...the eye sockets....Hmmm.
I suppose that it is probable that the Xenomorph once indeed did have eyes, but over the milennia the eyes became less than useful, and thanks to evolution, atrophied into nothing. Remember, the bugs are highly evolved creatures. If we are losing our appendix and the whales (originally land-creatures) lost thier legs, then why can't the bugs decide they don't need thier eyes? I suppose that would explain why the eye sockets are still there in the Skull.
Then, there is indeed the fact that the Xenomorph does use human DNA, or at least the drone from the original Alien move did. Perhaps it was simply a redundant genetic trait taken from the humans?
Still, who really knows for sure? Anything's possible, with the Xenomorph. Let's just hope Uwe Boll doesn't get his hands on the franchise for the third movie and find a way to answer the question.