The concept of middle name is alien to Far Easterners. When Japanese given names are translated into English, they are often in fact the phonetic translation of 1, 2 or 3 kanji characters all packed into one English word, referred as "given name(s)". Knowing that, you should be comforted to know that it is highly unlikely the missing middle name will cause any trouble in Asia.
In Spain, people are usually born with double surname - one from each parent. So for most Spaniards, their birth certificate and many of the ID contain 2 surnames + 1, 2 or even 3 given names - confusing to say the least to many foreigners. But many Spaniards chose to go by a single surname as they become adult, usually, but not always, it's their father's surname. So it's not uncommon so and so go by ABC XYZ instead of ABC XYZ-DEF. I think airlines have seen it all, it would be hard to imagine airlines struggle with all these variation of names and customs.