Barristan has to talk about Rhaeager with Daenerys at one point. Having a badass honourable person talk highly about Rhaegar should at least have people questioning the events...at least for those who remember who Rhaegar is.
And Jojen has said he saw Robert's Rebellion with his greensight in the show. If necessary he could tell more than just the Knight of the Laughing Tree story. Or have Bran learn about it when his greensight becomes more powerful. And who knows what Jojen's father will be able to tell if we ever get to meet him. So while I think it's too bad that the viewers couldn't have had more clues (Tower of Joy, House of the Undying) they still realistically have 4 years before Jon is actually revealed to be part Targaryen, if at all, and ways to drop hints before it.
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