Just keep in mind that the existing NOOK Apps don't have all of the features of the dedicated NOOK devices. You'll lose Read In Store, for one. You may (will, I think) have troubles with some magazine subscriptions. If you don't care about those things, it will work nicely for normal B&N ebook reading. * * I use Android myself, so can't speak to the Apple version with any authority. The exact capabilities of the iOS app may vary.
+1 to everything bobstro brings up.
I do use the Nook app on our iPad Minis on occasion (usually when I run out the battery on my NC), and for plain old reading it works fine, but I don't do magazines or comics, just text (with an occasional map).
If you sideload a lot of books, though, it's a bit painful to make them conform to the file convention the Nook app requires, as I recall. Those are probably better off in iBooks, though I have a friend who uses a third-party reading app and raves about it (naturally, I've forgotten the name).