Not sure what yo are complaining about. When you accept the app, there is a list of 'permissions'. If you do not like the 'permissions' do not install the app. One such 'permission' is modifying storage.
Every app that uses a data file of some kind needs to put the somewhere on the phone! I am not sure why you are singling out the NOOK app, as this is common practice.
The books have to be stored somewhere on the device. On My OG Droid, the Nook books were on the micro-SD card, while on the Droid 3, they are in the 16gb internal storage.
I wish that the developers of the apps would update the app to recognize the existence of 2 storage areas (sd cards), as is found on the Droid 3 and other phones, enabling you to choose which sd card you want used, either internal or external.
Bob