There's a lot of history behind this ruling and it goes back to two major cases from the mid-90s.
One of them involved the PlayStation version of Tokimeki Memorial. Getting the main girl in that game was extremely difficult so some company sold memory cards with hacked save data that gave you maximum statistics so it was much easier to get the best ending. Konami sued them and won. There was also another case where a strategy guide for a PC Romance of the Three Kingdom games included a disk with a program that let you hack your own save data. This, however, was ruled to be legal. There were some inconsistencies, but the gist seemed to be that game save data was copyrighted so it couldn't be sold separately, but actually hacking your own save data was OK enough, at least at the time. But probably it's more likely because the console business (and Konami) was much larger than the PC business and Koei. So like the rest of this thread suggests, it's a very pro-corporate ruling.
Anyway, remember when Nintendo sued Galoob over the Game Genie, and the US courts ruled in Galoob's favor? Imagine a world where the courts ruled in Nintendo's favor instead, so that basically set the landscape for cheat devices and modding in Japan.
