Your Kindle books are not related to the iTunes and Apps store. Kindle books are stored on Amazon's cloud, so you might want to give them a call and ask them if changing your iTunes & App Store on your iPad would affect you access to your Kindle books bought in the American Kindle Store, but I don't think you need to worry.
In your Kindle App, if you go to the Library and click on the set of little lines in the top left-hand corner, you will see the Settings option at the very bottom of the list that displays - tap on that. At the top of the Settings screen you will see the Registration info. Your device is Registered to your Amazon account in the Amazon Store. So, again, changing your iTunes & App Store will not affect your device registration on the Amazon site.
The books that you have purchased for your Kindle app will remain in the Amazon cloud and are accessible from any device that is registered to that account. I have my Kindle Amazon account set up on both of my iPhones, my iPad, and both of my Kindle devices. All of my books are accessible from any of them.
These are two different and separate functions, so you should have no issues. But again, you need not worry, because they will still be there in your Amazon account no matter what.
Best of luck,
GB