So, assuming without a doubt that Moriarty is dead - where did his body go? Was it found? Why isn't there any mentioning of that?
shareI don't think it needed explanation. Sherlock could easily have informed Molly about the unexpected development and she would have sent people up to deal with it.
Yes, I think it's the elephant in the room. Questions about whether Moriarty can really be alive would have taken a different dimension if we had known that Moriarty's body was found on the roof. I think that Moffat and Gatiss have deliberately withheld this information to encourage more speculation about how Moriarty could be alive.
shareI still think Moriarty is dead dead, we did not see his body taken away. But... like the Dead Bride he has for sure some network that will work further, we remember in start of season 3 how Sherlock went to Serbia to uncover a part of this network
shareconsidering all things leading up to that point, how could he have pulled off a fake suicide? with sherlock seeing all the details and all... nearly impossible.
shareThe events on the roof formed the story given to the public in order to convince Moriarty's empire that he was truly dead. Instead he was captured and held in isolation until the assassins contracts were fulfilled by Sherlock falling from the roof.
The public is now convinced that both are dead, leading to the destabilisation of Moriarty's empire and Sherlock's infiltration of it.
Just the knowledge that Moriarty is alive might be enough to trigger contingencies he himself created to leverage his freedom. So keeping his current state an absolute secret would require the involvement and resources of Mycroft who is aghast that his work may have been undone.
Then there is Redbeard. A topic that Moriarty would have learned about through Mycroft, but not something that Magnusson would likely have wanted or needed to know about. And yet he did.