I never owned a Nook HD, however, a co-worker did and she switched to a Samsung tablet. Had no issues transferring books to the Nook app. In fact, she said it was very easy. So, I'm sure the same will be said for the N9.
In regards to cases, I always feel they are a personal preference. I purchased three different ones for three different needs. I bought the Folio Keyboard case when it was discounted and it is wonderful for keeping the N9 protected and its keyboard works like a charm. Makes you feel like you have a laptop. I also purchased an inexpensive
FYY case from Amazon for 8.88 and it is perfect for transporting the device when the folio keyboard isn't needed. Lastly, I did get the magic cover to see if I'd like it. It is good and very minimal. It doesn't fit around the N9, but is a single side cover that connects via magnets to the tablet. I am keeping it since it allows for several viewing positions (origami), and it allows me to show off the beauty of the tablet.
Hope this helps!
J