Hi,
HikaShop is written in English (en-GB), and every other language, en-AU included, is a translation file loaded on top of that English file. Any text the translation does not carry keeps its English wording. Disabling en-GB in Joomla changes nothing there: HikaShop's English file is always the base, and it is not tied to the en-GB language of your site.
Three things worth checking:
1. The version of your Australian file. Open HikaShop > System > Configuration. If a warning about the language file appears at the top of the page, click the link in it to load the latest one. A file left at an older version has none of the keys added since, and those display in English.
2. The file itself. PHP refuses eight words as keys in an ini file: NULL, YES, NO, TRUE, FALSE, ON, OFF and NONE. One line such as:
in language/en-AU/en-AU.com_hikashop.ini or in language/overrides/en-AU.override.ini makes PHP drop the whole file without a word, and every text in it goes back to English. A key containing one of ! | & ~ ( ) { } $ " ^ does the same. Setting Debug Language to Yes in Joomla's global configuration makes Joomla report the faulty file instead of staying silent.
3. Where your overrides are. Translation overrides are per language. Joomla does read en-GB.override.ini on a site running en-AU, but only as a base layer, which any text defined by the en-AU or the English file of HikaShop then replaces, and that is nearly every text. So on your site the overrides have to be in en-AU.override.ini. The translation editor of HikaShop, the pencil next to each language in System > Configuration > Languages, writes them there for you.
The emails are a bug on our side. When a notification has to go out in a language other than the one of the page, HikaShop switches the translations and switches them back afterwards by loading the previous language on top. That only brings back the texts the previous language actually translates, so everything it leaves to English, and every override you made, kept the wording of the notification for the rest of the page and for the notifications sent after it. I've made a patch for this on our end. Download the install package of HikaShop on our website and install it on yours in order to get the patch. Then, you should not have the override issue you describe.