Guesstimate based off the size of most of my epubs, roughly 500 books. My average epub size is maybe 500-600kb, somewhere in that range (some as small as 200kb, some as big as 1.2mb). So with a little less than 250MB of user accessible storage, that gets you somewhere in the ballpark of 500 books. If you use Calibre though, it'll be a little less. It uploads a thumbnail folder with thumbnails for each epub, that I guess the nook can read. The images aren't big, but it adds something like 15-50kb per file.
Maybe call it 400 books on the low end unless yours are big?
At any rate, I have a fairly large wallpaper folder (around 20 images, about 300-400kb an image) as well as somewhere around 150 books in main memory and I have 150MB free of the ~250MB total. I have about another 30 books on the SD card and 3 books in the non-user accessible storage space since I bought them from BN.
A) My Gods that would be nice to have the option of that, especially once you get in to the big lists
B) It would also be really nice, but just A above would do most of what I'd want in B (easy enough to check under each author that all of their books are checked for the shelf in question)
Calibre will setup folders on the nook itself when you transfer files over to it. When in your library, select My Files and go to either main memory and books or SD card and book and the files will be sorted in their respective author folders the same way Calibre stores them on your harddrive (so make darned sure in the file meta data in Calibre that all books for an author really have that authors name, and not some derivation of it, otherwise you'll get multiple folders for the same author). I am 99% sure you can change this default behavior of Calibre so that you can sort them in to Genre folders and then author folder within the Genre.