Just last week, on Tuesday, February 26th, 2024, news broke out about the Yuzu emulator team being sued by none other than Nintendo themselves, with Nintendo claiming that the emulator apparently allowed users to play certain games early (due to street dates being broken) and also allowing...
Japan has some pretty convoluted IP laws, if Nintendo doesn't aggressively pursue ANY whiff of IP infringement, they might lose their exclusive rights. From what I hear this mainly has to do with bios and copy protection technology.
So hypothetically, if it can be proven that Nintendo is aware of an infringer and does nothing, then they might lose their protections.
I think it is more likely that both policies arose from a fundamental aspect of Japanese culture that has persisted through the ages, flowers from the same tree, so to speak.