That site is really funny, but I think the choice of colors in SMB and basically any other NES game was because of the NES capabilities at that moment, another reason why I personally think that Link and Samus had always been intented to be blonde, but the NES graphical capabilities didnt allow a good representation of that, imagine Samus without her brown hair in the original Metroid and with a yellow one, it wouldnt look ok at all, the same with SMB, red offers a perfect contrast with the blue sky or the black castles.