Nintendo will allow paid DLC in the future on 3DS and Wii U
However they probably wont use it very much themselves
Nintendo CEO Satoru Iwata has revealed at a Q&A session at Nintendos Toyko briefing that paid DLC, among other things, are headed to Nintendos digital stores soon. Both 3DS and Wii U titles will soon be able to support paid downloadable content in the future.
Nintendo wont be using the system themselves though; its more likely that third parties have suggested or requested this feature. Nintendo says it might offer extra levels or features via paid downloadable content but "low quality paid download content" like stat increases and keys would not be offered from Nintendo. They feel that while its a good quick way to make money, it can damage the relationship with their customers. So no different Mario hats for you to buy then.
Also on digital content, Iwata has said that the eShop and online has been used much more than on the DS but still not enough. He also notes that only a fraction of people so far have actually paid for content. Nintendo are working on it though and are hoping to increase their digital business by 5-10% over the next three years.
Look for more things from Nintendo in the online space soon.
Source: Andriasang