The kabushiki kaisha "kk" may be a necessary solution in certain situations (for example, to satisfy corporate governance requirements) but it is not especially tax efficient. "But those Japanese business myths tell me that 99% of Japanese companies are set up as kabushiki kaishas" you say - agreed, but 99% of those kabushiki kaishas are 'mom and pop' shops with no profits left after mom, pop and suppliers have been paid and 99.99% of them are not functioning at the subsidiary layer of a global corporate structure, i.e. tax efficiency was not a consideration in their choice.
A kabushiki kaisha may be a good choice for a Japanese customer liaison subsidiary but is not the best choice for a Japanese subsidiary distributor unless your costs of doing business in Japan are high and your Japanese margins are low. Unless you try to use an inflated transfer price (which a tax audit will look for) you will have Japanese profits that can only flow back to the foreign parent as post-tax (i.e. less 42% income tax) dividends which will then presently lose a further 20% withholding tax less tax treaty relief (although the new US-Japan tax treaty will eliminate the withholding tax for dividends paid to a US parent holding 50% or more of the kabushiki kaisha's stock).
A less well-known tax inefficiency of a kabushiki kaisha is that if directors are paid bonuses then those bonuses are deemed to be paid from profits, even if no trading profits were made (i.e. the KK is a customer liaison office). That means that if you pay your directors a $200,000 bonus you will incur an $84,000 corporate income tax charge even if the kabushiki kaisha operated at break-even. If you do incorporate a kabushiki kaisha as your Japanese subsidiary and want to pay your directors performance related bonuses, then structure their compensation based on an annually fixed 'divide-by-12' salary package which assumes a certain performance level. In the following year you can then retroactively increase or decrease compensation depending on the actual performance achieved.