Shota Horie more than held his own at hooker for the Rebels.
This is a weird argument you guys are obsessing over. There are big and tall Japanese people, just like there are Dutch jockeys. Averages are pretty irrelevant when you're talking about such a large population. And not everyone that represents Japan is ethnically Japanese anyway.
Plus, rugby isn't necessarily won by the biggest and most powerful team. If it was the Springboks would never lose. Japan have their own unique style of play based around speed. What they need to improve is simply greater exposure to a higher level of play. They'll get that in Super Rugby.
Finally, if you'd followed the Japanese team at all over the past couple of years you'd know one of the strongest parts of their game has actually been their scrum. They brought in a French scrum coach, he changed the conditioning of the front row players, improved their physiques and a year or so later they were pushing the All Blacks off the ball. You can see the very noticeable improvement in this video: