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First, rooting only gives you access to the operating system. You've replaced the operating system. You replaced (or flashed) the stock ROM with a "modded ROM".
Your books and magazines of course will show up in the Nook app, but unfortunately, your apps are gone. I've had an Android phone for a while and have bought all my apps from the Play Store. I only bought one or two apps from the B&N app store, so no big loss. If you have lots of apps, you might want to consider going back to the stock ROM.
There is a way to install apps on your SD card. It's a hack. I've done it on my phone, but right now I can't remember what to do. You could try Google searching.
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