Did Miraak ever know about the Nedes to the south of Skyrim and their Ayleid enslavers?
Two things for this one.
1. My friend Lleralyn is half ayleid and proof that not all of them are the exact same way (I know you never said that but I wanted to be clear that I'm fully aware there were ayleids with a different mindset) . Their father broke off from the rest of his people and took those that followed to the land of the Direnni, Bjoulsae, where he met the future Queen Nefrenya. A woman of striking beauty and grace (I met her personally, she became family to me after some time. She was a wonderfully kind woman and devoted to her kingdom and those she considered family.)
2. To actually answer your question, I believe he might have known about them but I doubt he paid much attention as he would have been occupied with situations within the dragon cult.