The only way Aemon would have known is if he was somehow in contact with Bloodraven (who would've been his great uncle). I doubt he knew. I think Aemon lost contact with him when Bloodraven disappeared during a Ranging mission. I think it was one of those things where Aemon ironically mentored a boy who without his knowledge was his great great great nephew. I think him being blind is a plot device, as even with dark hair, old Aemon would notice similarities between Jon and people from his family.
@dora_da_destroyer there's a lotta hints in the show about Jon's heritage. People just wouldn't catch them if they aint watching closely. There's the fact that Ned is described as a "square" by basically everybody who knew him and the fact he got a side chick pregnant is highly unbelievable When him and Bobby B are trading their sex stories, Robert couldn't even remember who the broad Ned fukked was and Ned wouldn't even talk about her. When Oberyn comes into King's Landing and talks to Tyrion, he doesn't say that Rhaegar "kidnapped" Lyanna like Robert said over and over. He says when "Rhaegar left my sister and ran away with that other woman," implying that he didn't rape her but, she ran away with him willingly. Then when Littlefinger is in the crypts with Sansa, he all but admits that Rhaegar and Lyanna were in love. That is was some tragic romance. After Ned killed Arthur Dayne, you hear a woman screaming out from the tower....childbirth? The secrecy about Jon's mother is....odd. If he's just a regular b*stard, why keep it a secret? What's there to hide?
Ned letting his "son" join the Army essentially knowing he is giving up his life basically is.....odd. In reality, he should've told Jon to wait a couple more years first. Or he could've married Jon off to one of the smaller northern houses or groomed him to serve as Robb's second in command, unless, it's best for Jon to be where people can't hurt him? Then there's him getting so mad at Robert for still wanting to kill Dany and Viserys in season 1. You could argue it's because he hates violence towards kids, or because he has a nephew to protect. There's also Jon's relationship with Ygritte, which sorta parallels Rhaegar's relationship with Lyanna. They loved each other but, were on opposing sides. Rhaegar was already married with a family. Jon swore to never have one. They could play house with each other for a little while in a castle or in a cave but, to the outside world, it could never happen. Then there's the common sense that Jon's arc is too important to be a "nobody". There's also the fact that two Kingsguard were protecting a tower in the middle of NOWHERE instead of fighting in the Rebellion, protecting the King or protecting Dany and Viserys. WTF? What are they doing there? Arthur Dayne is the best fighter to EVER LIVE.
EVER! Why is he being wasted guarding some castle in nowheresville? What's up there? Who's up there? There's alot of clues.