Amazon also has an account system where you put money into an account that is for another person, let's say your child or significant other. Then they can use that money on anything at Amazon.
Also, Amazon is a lot bigger storefront than the Nintendo eshop. Many more people are familiar with it and know how to navigate it as opposed to the eshop where some are likely afraid to search through it.
Ultimately, it's just another way to buy the digital games from Nintendo and I figure more options is always better than less most of the time.