All you could do is write to them and just see if they'd consider. An average person isn't going to get their idea heard by Nintendo, so it'd have to be someone from DuckDuckGo itself.
That said, right now all there is to choose between are Google or Yahoo. See: https://en.wikipedia.org/wiki/Internet_B...
Sure you can enter in URLs and get to whatever site you want and as best as the 3ds can render it but that's not the point. On a device that has around "Worldwide: 42.74 million" units sold, how many of those people do you think even know anything even exists besides Yahoo or Google and why shouldn't they benefit from the same privacy/security benefits as the rest of us with other choices? (especially kids just trying to look up a game guide)
DuckDuckGo itself works fine from what I've experienced on the 3DS. I'd just have to hope that Nintendo didn't pick Yahoo and Google only as some sort of paid perk thing. I don't know, nothing groundbreaking here but I thought it'd be neat if it happened.