Have a HAF-X myself, yes you can have both at the same time. You can even keep the side fan duct on as well if you turn it so the cutout lines up.
My rig a fair while ago, very different looking now
Top Tip: Undo the "screw" in the VGA holder and re-assemble it so the handle is on the bottom rather than top. Looks far better and still has the same functionality.