Disclaimer: I'm doing this for fun (though not very well I admit), no profit nor do I claim any ownership of the show.
Watson wasn't stupid by any means. Doctor, soldier, neither allowed for being particularly stupid. Though, eyes flicking briefly to Holmes lying naked and slightly out of breath next to him, prehaps he was foolish. He knew what they were, collegues with a very strange friendship. He knew what Holmes was, after all he did shout it at the police. He knew what he was and knew Holmes had probably seen his mental issues even before suggesting they share a flat. A co-dependent and a high functioning sociopath sharing a flat, were partners sure but not in that sense. Not 'together' regardless of certain opinions. John rolled slightly to the side barely listening as Sherlock muttered under his breath some of the equations from the latest case compleatly oblivious to the open curtains, the clear day or his naked state as he jumped off the bed and started pacing. Sherlock blinked before running to the front room. Aha a breakthrough then. John lay back waiting to be called to move into action or to offer Sherlock a brief distraction whichever came first. No John wasn't stupid. He also knew why Sherlock chooses to have sex with him. It's the same reason he was allowed to move in, to go to that first crime scene and to carry Sherlocks credit card. Convinience.