It certainly seems strange. But maybe the demand from a relatively few Japanophiles doesn't outweigh the adminstrative costs of maintaining a much larger number of SKUs (including regulatory requirements) and they'd send boxes of green tea chocolate to go out of date on shelves. I'd have thought a big corporate would have pretty scalable product range management but maybe it's just cheaper to hand that off to importers. Some calculation must presumably be involved.
Though I like to think the Nestlé/Hershey executives have been threatened by immaculately-suited Pocky-toting enforcers of the importers making profits on the novelty arbitrage.