Realistically, this won't affect their sales numbers significantly. Even if tens of thousands of hardcore fans boycott the game, that's just a drop in the bucket compared to the millions of casual fans, kids, and new players who don't know/care about the controversies and are going to buy it regardless.If anything, the sales taking a hit might be the only thing getting TPC to examine their handle of the franchise, only because they have to answer to investors and owners (Nintendo?).
Plus, and this is just an educated guess, but I don't even think the games are the franchise's primary moneymakers anymore? The amount they rake in from the anime, manga, toys, plushies, and merchandising deals probably dwarf the games' sales, and those are going to remain steady even if the games become irredeemable trash.