I have a Nook simple touch and with an SD card inserted I have 7000+ books(thanks Mobilism posse ).
The only problem is the Nook software wasn't designed for that number of files, you have the search function obviously, but scrolling through my collection is the definition of laborious, for example you can't got to all the the books starting with a particular letter, you have to scroll five books at a time form A to Z.
You CAN make 'shelves' but the don't seem able to handle more than a few dozen books before the device starts acting up.
I've searched the web but to no avail.

This may be a way to avoid looking through too many books looking for something to read.

On my SD card under \My Files\Books, I put new books I want to read. I have other folders like \My Files\SF, \My Files\Nonfiction, etc... for books I have read.

At the Library screen, select "All" from the drop-down list will show all the books from all folders.

Select "Books" will show only the books inside \My Files\Books. Once I read the book and want to 'hide' it, I move it to a different folder.

Using this method, I went from having to look through 500 books to less than 30.

This works on software version 1.2.1. Please note that bookmarks and highlights are hard-coded to the filename and location, so moving/rename the book will make them 'disappear'.