Of these, I would only really be concerned about nxDumpTool, nxDumpFuse, and Lockpick_RCM as possible to come after using the same strategy, though. And even then, Lockpick_RCM was already taken down and mass redistributed.
It's not illegal to modify the hardware you own, and the rest of those aren't directly interacting with Nintendo's DRM-protected software. The only one that they could arguably go after is Atmosphère, but SciresM has held a very strong public pro-homebrew and anti-piracy stance which makes it extremely hard for Nintendo to argue that it's primary purpose is DRM circumvention.
I plan on making offline archives of Hekate and Atmosphère at some point, in either case.