I'm not sure why your books aren't showing up on the Barnes and Noble website for you but, as for your Nook, I have a suggestion for you. I hope it helps! =)
If you go into your library on your Nook, try pressing the Sync button up in the right hand corner. I only suggest this because yesterday I purchased two new Nook books and they didn't show up in my library even though I had Wi-Fi on. So, pressing the Sync button "refreshed" my library, bringing my new books "into the fold" so-to-speak.
I hope this suggestion helps you! Good luck!