The Switch is supposed to be the 3DS' successor. And will eventually become THE portable gaming in Japan, I'd say it already is. You may think it's not fair, but that's just the way it goes.
And of course it's sold more because that's the system that has been out the longest and it's a Nintendo handheld AND the successor to the DS.
The Vita was a flop.
The Wii U were dead upon arrival.
The PS4, while doing everything it can and may ultimately outsell the PS3 over there, is not coming close to it.
And the Switch JUST came out.
I'm talking about launch specifically up to this point, and the Switch is neck-and-neck thus far and would be beating the 3DS convincingly if there was enough supply to meet demand.