In an interesting interview between Kotaku USA and a Nintendo PR rep, Nintendo delved more into their digital eShop.
When asked about the Nintendo Switch digital store being region-free, Nintendo revealed quite a lot about how this would work.
“The Nintendo Switch system is not region locked, but we recommend that players buy games within their region to ensure full service and support. The user will access the Nintendo eShop that corresponds to the country identified in their Nintendo Account. (Up to eight user accounts can be created on a single Nintendo Switch system.)” said Nintendo’s PR rep.
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Another words if you want to buy games digitally from another region Nintendo will bump the price?
In other words, similar to the PSN store... If your account 'happens' to say it's from Japan, you buy it as if you just moved several hundred miles away from where you are.