"So going by your logic if DQ in Japan = money then wouldn't DQ on more platforms = even more money? seeing that Sony & Nintendo each own about 50% of Japan. "

No going by my logic NINTENDO made sure that they could attract their folks to their console. This exclusivity surely came at a price( I take it's the publishing rights). Over in JAPAN they already love DQ so why wouldn't they just buy a Nintendo for it?
It's a super win for Nintendo and a win for SE. DQ sells a lot in Japan. Meaning that Nintendo will surely Sell tons of WiiUs( and a few Wiis along with it since it will be sold earlier than the "defined" version which will be published for WiiU) just based on DQ in japan alone.

"ignoring 50% of the total consoles/handhelds in Japan seems like a pretty bad business decision."

How Is Sony not getting money from DQ affecting Nintendo or SE? We aren't talking about SE or Sony.
It's in the end still business, and a title like DQ are bound to sell sh/t tons regardless of the console/handheld.

Nintendo took it just like how Sony took the FF franchise since the Playstation days.
You want to talk about fair? Go see people who have NOTHING.