Because I think this is why John holds out hope, why he asks for one more miracle. Because he knows, and he knows well enough to not let on.
John knew that Sherlock wasn't dead. Couldn't possibly, unless he'd been dead for hours before he'd jumped and that was just impossible. It was implausible that someone could have survived that fall, but it was impossible that the body he'd seen and touched was his flatmate and friend. His best friend with his brilliant mind and his carefully concealed humanity.
When he'd been in Afghanistan they'd had a three day battle over a small village, and once things had settled down—the people they'd been fighting just ghosted away in the night, leaving the village empty and the people there dead—John had gone in with some other doctors and medics, looking for survivors. He'd touched many dead bodies that day, bodies which had cooled over-night after their deaths. In his other work with the unit John had also touched many bodies of men who'd just recently died.
The body smashed on the pavement outside of Bart's was most definitely dead, but it had been dead for hours. It was stone-cold, the flesh stiff. If it had been Sherlock it would have been at least a little warm—he was wearing his coat, after all—and the skin would have been springy with just-departed-life. John knew he'd been disoriented from when the bicyclist had hit him, but he believed he could tell a long-dead body from a freshly-deceased one.
Sherlock must have done it for a reason, though, tried to trick John—so John played along. It wasn't hard. His best friend was still gone amid horrific circumstances to where John knew not, and the knowledge that Sherlock wasn't dead meant it was too painful to go to Baker Street anymore. He acted like Sherlock was dead because he had a hunch that perhaps Sherlock's 'suicide' had had to do with Moriarty. The madman had probably threatened to kill those Sherlock was close to, the people he cared for despite his ardent efforts otherwise. Perhaps that had been the deal—die so that they might live.
But Sherlock had outsmarted him, because Sherlock was fantastic and amazing at problem solving.
John knew this because Sherlock wasn't dead, couldn't possibly.
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