In a 1985 interview with Bill Gates published in the 8/83 issue of LOGiN magazine, he stated the "X" letter in the MSX name doesn't have any special meaning. It was added purely for aesthetic reasons that he felt the logo needed to look good, and that it had an almost artistic sound and a nice ring to it. He thought the logo captured their distinctive style, and that it acted as a "guarantee of compatibility" when systems compatible with the MSX would start using it.
Contributed by ProtoSnake