Thank you all for your help. It's a great relief. I had a reply from a woman on a Japan forum that has the parenthesis on her passport saying she used only the "Suzuki" and had no problems. Maybe for the sake of convenience we'll use just that, so we can use the automated check-in. On the other hand, hearing someone's gone through 30 times without problems makes the full name a reassuring thought.

Now I just have to worry about her going through security and customs without speaking English...