If Sakurai was prejudiced towards the West, he wouldn't love Minecraft as much as he seemed to in his article, saying he doesn't usually go back to games he's completed (yes, you can't really complete Minecraft but I assume he means he's played it a lot before/he beat the Ender Dragon). There are other Western games he's played as well, such as Undertale, and if he was truly prejudiced then Shovel Knight would've just been a Spirit alongside Shantae if he bothered adding them at all (and I really don't see why either of them would've been the first Western-owned character, anyway). K. Rool and Dark Samus, while they are owned by Nintendo, were made by Western developers, so if he had any real Western prejudice then he would've probably been reluctant to add them or even ignore Western fans who wanted them alongside the outcry for Ridley (of course some Japanese fans wanted them as well, but for Ridley in particular he specifically mentioned Western fans).
As I said, he also considered Banjo-Kazooie for Melee, knew fans saw them as a natural inclusion, and he said there were would be legal difficulties involved with trying to get them (because of the Microsoft buyout; also, even when with Nintendo, they weren't fully-owned by them). Nowadays it seems there wouldn't be much of a problem, so if there's anything holding back Western characters then it's simply because of there being more Japanese gaming icons (as is the reason Pac-Man and Mega Man obviously got in before any Western character, and Castlevania was highly requested and is iconic itself), or maybe even Sakurai being afraid of potential translation issues (though this seems unlikely given how he acted at E3).
Maybe he prefers some characters over others, sure, but that ain't prejudice, and he still takes fans' desires into account. If B-K did well on the Ballot and Sakurai is considering adding a Western character, then they would be very likely. He may not even see it like choosing Western or Japanese characters and actually considering that, just picking whatever character he thinks should be in.