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Are the books on the SD card? If so, pull the SD card out of the Nook and put it directly into a card reader attached to your PC. The Nook will be out of the picture at that point and thus not able to hide your books. Same thing goes for something like a Fire HD tablet. I have a file manager on my Fire but it could not see my books (even though the Kindle and Nook apps on the Fire could see their respective books). Pull the SD card, taking the Fire out of the picture, and you can access the files (provided they're on the SD card of course). They will be DRM'ed, but that is not a major roadblock. But we can't discuss that aspect here.
There is some USB protocol that can be used to selectively display/hide contents, but I forget what it's name is at the moment. When you attach the Nook/Fire/Kindle/etc. to your computer using it's built-in USB port, the device can invoke that protocol to hide things from you. Taking the device out of the picture by yanking the SD card and inserting it into your computer directly negates the use of this protocol.
This is exactly how I got my Nook books after B&N took away the ability to download your books to your PC. I installed the Nook app on my Fire, and used that app to download all my books from B&N (they allow that, since you're downloading to a Nook app and not to a PC). I couldn't see those books on the Fire when using a 3rd party file manager. But the Nook app could display them, so I knew they were there .. somewhere. When I pulled the SD card out of the Fire, I could see the (previously hidden) files after the SD card was plugged directly into my (Linux) computer. It should be the same on Windows/Mac if you're not running Linux.
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