Could be they rebuilt the base with an exact floor plan so that way in time of an emergency you'd know your way around. Also, they could pull a switcheroo with a scientist, say make them think the crazy device they are working on is the area 51 base in neveda, but really they are either on the moon, some gaint space station, mars perhaps, and lastly, if it's a USA base up there and you have nukes, I wouldn't point them at our own bases(I would guess a 115 antidote war head/payload like the VR-11, but there is still zombies in no mans land. Then again like I said maybe the (antidote loaded?) missiles didn't hit around area 51. But I suppose we will never really know.