I do have a feeling that the website containing all the 3DS title keys will receive a C&D notice from Nintendo, freeShop certainly won't be the last Homebrew app to be targeted, I can guarantee you that the Homebrew Launcher website will also receive a C&D notice from Nintendo, just because "it uses exploits that circumvent hardware protection and security measures and creates a loophole for piracy to be created". Enterprises can either be very nice, or very nasty when it comes to protecting their IP, and the enterprises will get away with it because it perfectly fits into the violations of copyright laws in any country, even the US.
There's nothing we can do to stop them, all we can do is defend ourselves. Anyone (such as myself) who really wants fan games and Homebrew to remain safe and to replace copyright law entirely with something completely fair and balanced, as well as a new type of entertainment economy where the government pays for the digital content instead of the consumer, should beg to the government or vote for candidates during elections that well and truly support ROM hacking, reverse engineering, fan games, free speech and copyright law removal to replace it with something fair and balanced. Copyright law is ancient and completely outdated, it was only useful back in the days long before PCs became available. Instead, politicians are trying to revive copyright law that never works in any way, shape or form and destroys the economy, imo.
Switch runs on a chip based off Nvidia Tegra X1. In other words, it's modified and will be very different from the original model of the Nvidia Tegra X1. And I wouldn't be surprised to know if it protects it's bootrom with a series of encryption keys. In fact, it probably won't even be called a "bootrom", it's more than likely it would be a series of startup sequences on different sections of the CPU. There were limitations on what developers could do using the 3DS CPU, because it was designed in that way at hardware level.