What's sorta funny is that Jon is clearly the chosen one and is actually in position for the show to do a pretty big 'subverting expectations' shtick with him. He's practically a caricature of Ned and the show has gone to great lengths to demonstrate that being any kind of a good guy gets you and everyone around you murdered horribly, or at least your life turned upside down, and he wasn't even an exception considering how his tenure as Lord Commander ended. So the show could sorta turn things on their head with a 'no all you scheming backstabbing fucks fail and the goody two-shoes wins'.
There's also the question of whether Sam and Bran actually reveal the truth of Jon's parentage, if they are believed, how widely it gets revealed, and then what the ramifications are. In no particular order of importance:
As a trueborn male descendant of Ned's father, Jon's claim to Winterfell/House Stark probably supersedes Sansa's. This is largely a moot point since she's already stood aside in his favor, and even if finding out that he was a Targaryen caused her to change her mind, her only trump card was Littlefinger's command of the Vale, which she already played. Her only remaining importance is a marriage alliance, and I honestly kinda wonder what's gonna happen when she crosses paths with Tyrion again.
The North knows no king but the King in the North, whose name is Stark. Jon is not a Stark, he's a Targaryen. Even if it became widely known that Jon is a Targaryen, I honestly don't think there's enough time left for anyone to care about this one with the giant army of the dead descending on Winterfell.
Jon and Dany realizing they're Aunt and Nephew after fucking like rabbits for at least a month or two on the trip back to Winterfell. The supreme awkwardness of this is why I think there's a very real chance that they'll just never reveal Jon's parentage in the series and the Tower of Joy scene will end up being nothing but fan service.
The Iron Throne. Simultaneously the most and least important ramification of Jon's parentage is that he's the rightful heir to the seven kingdoms. It's plain as day that he's the reluctant hero archetype with no interest in pressing his claim to the throne, especially against someone that he's madly in love with and has sworn fealty to, but knowing that another trueborn Targaryen exists might result in Dany heroically sacrificing herself to kill the Night's King. There isn't enough time left for the angle of political intrigue/disaffected nobles latching on to the fact that she isn't the rightful heir.