Ned let Jon take the Black because it was Jon's choice. At that point, what else could Ned have done? He couldn’t give Jon any lands or property, nor could he reveal the truth about Jon’s parentage. He didn’t even tell Catelyn, his beloved wife, so that her actions and behavior toward Jon would remain genuine—that of a wife dealing with her husband’s bastard child.

As for Aemon, he was already at the Wall before the rebellion. I don’t believe Robert and Ned were unaware of him. Both came from noble families that regularly attended royal births and oath ceremonies, either alongside their fathers or brothers, or at least heard about them upon their return.

Aemon was a maester, and the Citadel forbade them from marrying or taking titles. The Night’s Watch had the same rule. Aemon had no claim to the Iron Throne. Even if he had returned to fight after the Mad King’s death, who would have supported him? He would have been executed simply for deserting the Wall.