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No one outside of B&N themselves know what the update or the App store will offer. I would be surprised if the Kindle app is one that is available in the store.
As for rooting, I rooted mine within moments of buying it. Rooting simply "unlocks" and opens up the underlying Android operating system that is already installed. All of the original software is still available. (others go beyond that by installing custom firmware containing different versions of Android... THAT's where things get more involved)
Using autonooter is very straight-forward... not much more complicated than the process of copying files from a digital camera's memory card. It's an all-in-one patch that roots the system, and installs the Google experience apps (mail, maps, market, etc.), and app needed to emulate the hardware buttons that a full Android system expects.
After autonooter is applied, you end up with the stock nook color user interface and all new apps (and those installed from the market) will appear in "Extras".
So at the bare minimum, the net result is that you'll have a nook color that has more "extras".
But, most people don't stop there... they'll add a different user interface to give it a more tablet-feel rather than ereader-feel. I use Zeam, but there are others out there.
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