Then again I've heard that the Japanese have this magical invention called an "app" which someone can install on their phone to add new functionality.

I've even heard that there are some ones already for say the Tokyo subway.

There are lots of third-party transit routing possibilities (although many are not so great). Nonetheless, many people will use the defaults, and having to switch apps to do something which didn't use to require it is, of course, annoying. Basically, the phone sucking by default is not a particularly good business strategy.

My suspicion is that the Japanese resellers (au, SoftBank) will preinstall something better than Apple's map (maybe Google's rumored new mapping app). I've no idea how much freedom they have to do this under their contracts with Apple, though, or whether they could integrate such an app more deeply (e.g. cause it to be used as the system default mapping app).