I have a few hundred books on my nook. I soft-rooted my nook and sideloaded content is better managed than B&N content with the "My Books" app in the soft-root. My feeling is that soft-rooting a nook is a no-brainer, easy to do and easy to undo.
I converted all of my fictionwise content with Calibre and cleaned up metadata just for better organization, it looks good and I have no problems.
-Duncan
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