I think establishing that Daenerys cannot have children, and the dragon are her only children, and then revealing, nope she can have children with her dreamboat nephew is cliché in that it is the happy ending everyone would want. I personally liked Daenerys living an unconventional life (very Elizabethan too, yes) where she doesn't have children or possibly a husband, yet can rule gloriously and usher in a golden age.
We also know she cannot get pregnant since she was able to with Khal Drogo, but after plenty of trying with Daario Naharis and (in the book) her second husband, she never became pregnant. I admit that Jon Snow could be the loop hole since he too is a product of blood magic now like Daenerys post-season 1, and additionally Viserion has died which might have loosened the rules on Dany's fertility.
But Jon, Dany, and a baby ruling at the end just does not fit this show at all. And I am thinking maybe they won't got there, because they foreshadowed it too much, with even Jon wondering if she is wrong. If they wanted it to be a surprise, I feel like they would have only hinted about it once during the Tyrion succession discussion in episode 6, and not brought it up two more times after that.
But I am probably crediting D&D too much. Without Martin they really can be that heavy handed and obvious. But if they do get pregnant, that means one of them has to die, because this is not going to have the storybook ending. And in that case, my money is on Jon, because he has a hero complex and shows not a real interest or passion for ruling.