Hi!
Thank you for this post. Yes, I knew about this problem but you explained it in more details. For your reference, we are using the following Java library for conversion: http://www.kawao.com/java/kakasi/ and yes, we convert all Japanese symbols to Romaji - Katakana, Hiragana and Kanji. I can easily turn off Kanji in automatic transliteration but we don't have any [convenient] way to provide manual transcription at this moment. We are thinking about having it in the future though...
Chinese is a totally different story

- we use the following Pinyin library for romanization: http://pinyin4j.sourceforge.net/