I think it, and the others I mentioned, are there in stock, but you just don't see them in the standard B&N interface. I've upgraded through several iterations of manualnooter and saw at least some of them in previous versions. I'm not about to roll all the way back to non-working mn versions to test though, so you'll have to try that yourself.
Since it's something more of us are seeing, I think it's safe to assume it's supposed to be there, and I'd leave it alone unless it is causing problems.
I do see dev.nookreader-1.apk in /data/app with a matching icon, so I assume that's it. Mine is date 02 Mar 2012 (when I ran mn) and sized at 4.49k. I don't see a corresponding entry in the mn zip file under /data/app, and I don't see any shenanigans in /META-INF/com/google/android/updater-script, so I don't think mn puts it there. I've also got a mysterious B3AndroidReader.apk in /system/app I forgot to mention before. You could always ask
GMPOWER over on XDA if you're still concerned.
If you
really want to know what's on your device, you need to forgo using proprietary software like the B&N firmware and stick with open source alternatives such as CyanogenMod. Though I've used it, colchiro's the licensed CM guide around here and can probably answer most of your questions.