[Australia] Configuring a Macbook Pro 15" with a Japanese Keyboard

When I change the language to Japanese does it automatically assume that I'm using a Japanese keypad

No.

Will I be able to just buy a complete Japanese Keyboard and have it installed/install it myself and have it work correctly with the differently set keys?

Perhaps someone who has done this can answer. You have to get the hardware to recognize it is connected to a JIS keyboard, which might happen automatically or might not.

Are the keys even set out slightly differently on Macs?

You can see the layout here:

http://support.apple.com/kb/HT2841

PS I wonder if this is worth the trouble. I understand that direct kana input is much less commonly used by Japanese typists that qwerty input.

i don't know how much this will help you, but here goes:

we have a macbook pro 13 2010 with the stock keyboard. my wife is japanese so we have the machine set up to switch input language at the top right of the display. she has never had an issue with how the characters come out. i've even used it myself to post some japanese. basically you just type a word how it sounds and the computer figures out what you are saying, if that makes sense. for example if i wanted to email my mother in law and i wanted to type the word "katakana" i would just type those letters and it would show up in the email in katakana characters. also, would you just be using katakana? i mean the computer uses hiragana and kanji characters as well. i'm assuming you know that katakana is usually just used for 'loanwords' i.e: words that are pronounced in japanese just like they are in english speaking countries. i know you said you wanted to have the katakana characters on the keyboard so i can't help you with that.