I wrote this question because I sent off a technical support request to Apple a few days ago, but hadn't heard anything back yet. As luck would have it (typical!) barely an hour after posting to SO, Apple responded, so I guess this is the authoritative answer (the second part about no localization folders is what we want):
The value of the Languages field in iTunes Store is created by scanning the localization folders in your application bundle. If you want it to show "Japanese" only in the store, you need to make sure there is only "ja.jproj" folder in your application bundle. If you don't even have any localization folder, you can select plist file of your project in Xcode, and set the "Localization native development region" by selecting "Japan" from the candidate list supplied by Xcode plist editor, by doing that the CFBundleDevelopmentRegion key will be set to "ja_JP" (language_local), you can also follow ISO 639-1 or 639-2 to use "ja" or "jan."
I will mark this as answered in 2 days when the time limit expires.
Additional edit: I suspect the Apple employee meant "jpn" in regard to ISO 639-2, as "jan" is not a valid code, but jpn is.