I understand there's a Newsstand app. I am wondering, however, if I were to purchase a newspaper subscription through the Nook or Kindle systems, will I be able to read them in the standard iPad (iPad 3, iOS 6) apps for each publisher?
One reason for concern is that years ago, I found that some things I'd purchased on the Nook — public domain books at least — we're invisible to the Nook Windows app. ( Newspaper edition purchases may too have been unreachable).
Best Answer
For the Kindle system, if one looks carefully under the product description such as you would find under this list, http://www.amazon.com/Kindle-Newspapers/b?ie=UTF8&node=165389011, one can see a link for "Available on these devices". This link will tell you if an Amazon subscription for that newspaper can be read on "Free Kindle Reading Apps", or exclusively on "Kindle e-readers".
In order to have the freedom to read on multiple devices (which seems to be the intent of your question, but forgive if I assume too much), you'd want to choose a newspaper available on "Free Kindle Reading Apps".