John never let himself think that Sherlock would die. Even during this whole business with Moriarty he didn't consider the possibility. Sherlock was not death. Sherlock was life and passion and excitement. He was not still or cold. If John hadn't been there, forced to watch his best friend kill himself, he wouldn't have believed it. He would have laughed off anyone who even tried to suggest such a thing. As it was happening he didn't believe it. Sherlock was bluffing. Sherlock wouldn't point a gun at John without a proper reason. Sherlock wasn't sentimental enough to leave something as simple as a note. If Sherlock were to die, he'd do it quietly, because despite all of the shows Sherlock put on, he was still a quiet man who didn't believe that he was worth anything, no matter how many people told him otherwise, because he's Sherlock, and when he goes into his mind palace he's greeted with every taunt and jeer that was thrown at him by Mycroft and Donovan and every one of his ex-classmates that weren't able to see past the bluntness and supposed freakishness to little brother seeking approval, the coworker who just wanted to help people, and the genius unable to understand others hiding underneath.
John catches himself forgetting that Sherlock is gone quite a lot. For the most part its little things; the surprise at the lack of body parts in the fridge, the dust collecting on the untouched violin sitting quietly on the desk. That's one of the few things John couldn't bear to give to Mycroft to put into storage with most of Sherlock's things. John even keeps making a second cup of tea. He'll bring it into the living room and, depending on how tired he is, he might sit down and start to drink his own tea, completely expecting Sherlock to reach out and take his own cup. During his more awake tea times he'll stop in the doorway, turn around, and bring the second cup to Mrs. Hudson. She's happy to drink it, even though it isn't even close to the way she likes her tea prepared, because even if one of her boys is gone, she's going to do her damnedest to protect her remaining child. Even if she's not nearly as perceptive as Sherlock was, she can see that John is in a bad place. The walls connecting their flats are thin, and several nights she's found herself kept awake by John's sobs.
In a way John was worse off for meeting Sherlock. At least before he didn't have all these memories taunting him with all the things they'd done, and all the things they were going to do. He does shut himself off like before. He goes to work, avoids social contact, and comes home at night. He stops talking to everyone except Mrs. Hudson and Molly when she stops by for a visit. They're the only two people who don't over-glorify who Sherlock was.