It's a comman practice to have the same numeric value that looks good and which are people still ready to pay instead of calculating the price acording to the exchange rate (for which btw. Nintendo most likely would use the Yen<->Target exchange rate instead of US$<->Target since it's a traditional japanese company) in appstores, eshops, ...
This also has to do with the fact that you don't want to change the price often just because the exchange rate changed (6.99 -> 7.13?).
E.g. in the euro-area it also is 6.99 (with taxes since they're always in the displayed prices here. But if one country makes that different I'm sure they just would go for 6.99€ + GST).
The numeric value only is changed where it makes sense. Either because 6.99 is really to low/high due to the value of the money e.g. 6.99¥ would be just ~0.08CAD, because it's uncommon to have odd prices in general in a country (then they could go for 7 instead of 6.99) or because a countries population is really poor. I assume the prices in russia e.g. are much lower (at least on steam they're), guess there're also south american countries with much lower prices.
