>>714602182
As far as the scenes shown off in-game are concerned, we never take a direct look up at Spire 4. So, it's not as if there was a scene were the camera looked up and showed no Demogorgon to contradict its existence. It's also kind of left a mystery what has happened to Spire 4 over the years from Lily and EVE's point of view.

Also, I guess it was cloudy that day.