It is part of his routine. Whenever physical necessity has led him to need sleep, he lies on his bed, lubricates his hand liberally, and masturbates himself to orgasm. The muscular relaxation combined with the hormone rush calms his mind and he is able to sink back into the mattress and gather a few hours of rest before his mind is up and racing again. There is nothing obscene or even sexual about it. Some people bathe before bed, or read a familiar book, or drink warm milk. Sherlock wanks.
He ends up thinking about the events of his day, during this period of physical stimulation. He does not have any sexual fantasies to go to, so he reflects on the cases, the deductions, the interactions that drove him from step to step and ultimately exhausted him enough that he was forced to resort to this (the sleep, not the masturbation. The thought of the wasted hours kills him). He does not try to answer the unanswered questions; that would keep him up longer and ignore the entire purpose of the exercise. This is more of an idle reflection, something to paint the back of his eyelids with as his hand grips the head of his penis before sliding back down the shaft.
And with the events of the day, come the people who made up those events. Anyone who he interacted with is just as likely to flit through his mind. Technically speaking, he has masturbated to the thought of Lestrade, of Donovan, of Anderson, of Molly, of countless anonymous detectives and lab technicians and homeless people and suspects and families of the victims. Thinking about them now means nothing more than thinking about them at any other time.
And John. He spends so much of his day with John that it is frankly inevitable that he thinks about him with his penis in his hand. He thinks about John standing over a body that afternoon, about John eating lunch at that good Chinese place, about John pecking away at the keys as he updates his damned blog. He thinks about John calling him brilliant, fantastic, amazing, a genius. He finds himself dwelling on those moments especially.
He is not exactly sure when his idle reflections become projections. Fantasies of potential things to come. Idealized situations, made up of brilliant deductions and unending admiration from short blonde men. Men who leans their bodies in closer and share their radiating heat.
On a strictly sensual level, he has to admit that it would feel good, touching John like that. Like sitting next to a radiator on a cold day. His hand grips tighter around himself, and he acknowledges that these feelings would most likely be stronger if it was a warmer, rougher hand around him. And he knows that inside of another man's body, it would be hotter and tighter than the grip of a hand. From that perspective, sex makes sense to him.
It is from every other perspective that it does not.
His body tenses and his back arches as he reaches climax, semen spilling out over his already-wet hand. A box of tissues on the nightstand means that he does not have to get up from the warm cocoon he has settled himself into, and he relaxes his head back into his pillow. A few hours of sleep and a shower in the morning will set him right again, and he will be free to examine reality once more, unencumbered by fantasy and projection.