I think it's going to happen and is exactly the transformation that Reggie was alluding to. They would eliminate inventory risk and control pricing so that games don't hit the Wal Mart bargain bin and hurt the brand perception.
Iwata recently ended a Q&A talking about how physical media, even in movies and music, are no longer selling. He clearly sees digital as the future, if you read the question
http://www.nintendo.co.jp/ir/en/library/events/150217qa/03.html
Likewise, Sakurai, one of his close friends, was recently on record as saying how much he admires Steam.
The NX will see much more variation in pricing for not only 3rd party titles, but Nintendo's own games. We've already seen them experimenting w/ different models. Nintendo will get around the credit card issue by expanding "amiibo" to other products and introducing more and more limited edition gift sets w/ software launches in store--they just won't include a disk or Game Card. Besides this, I expect Nintendo's structure w/ the new loyalty program and cell phone apps will keep parents/kids in the loop.
Losing the disc drives not only makes cross-platform play more natural, but it could make for a slicker console design w/ more airflow.
I believe the preparations are under way already with Amiibo and expanded licensing to both appease retailers and keep Nintendo fresh in the public eye as their games physically start to disappear from store shelves.