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http://www.nintendo.co.jp/ir/pdf/2014/140508e.pdf
Nintendo does give breakdowns on the sales of their games, not on their investors site but in the documents they release during their quartertly results, the one up there has WWHD for 90k on Japan, so its straight from Nintendo.

It obviously includes digital, digital is included in all games up thare (which is the 3DS games and WWHD)

And no, there's no data on how Twilight Princess on NGC did on Japan, that version failed to enter Famitsu's top 30 on the week it came out.