To my knowledge, LC_CTYPE shouldn't influence the language settings - just the "character type".
LANG is for setting language (menus, tooltips, manpages, error messages etc.) and LC_ALL sets all LC-environment variables including LANG.
But it's correct that you don't have to load a japanese locale setting to use scim with japanese input.
I'm using this combination for example:
(make umlauts work properly everywhere and use UTF-8, make sort order according to german dictionary sort order (influences programming languages like perl for example), but leave all language settings untouched in english - I hate translated error messages...)
To type japanese in romanji on a german keyboard with Anthy I use scim (scim-anthy) with this setting:
export XIM_PROGRAM="scim -d"
scim -f socket -ns socket -d
scim -f x11 -s socket -c socket -d
This setup - proper unicode-enabled font provided everywhere including Firefox - lets me type german, english and japanese with scim and shows japanese websites correctly. (And most other languages supported by my chosen font for that matter...)