From what I know, the Japanese eShop will pretty much accept any foreign credit card. I'm pretty sure that the Australian eShop won't likely support your American credit card.
If you're going for the Japanese version, I highly recommend you have some prior knowledge of the Japanese language if you don't like playing a guessing game on which button/command you'd need to press to progress. I recommend reading the OP of
that neoGAF topic and see if you'd rather have a Japanese New 3DS over the Australian one.