It's a lot harder to go after homebrew since there isn't anything directly linking atmosphere/hekate/etc. devs to the promotion of piracy.
Since the Yuzu team had a whole company formed to manage their patreon funds and were clearly promoting functionality for a game that hasn't been released yet, they were an easy target for Nintendo. The same thing happened with Team Xecuter's switch homebrew/mods ages ago.
If Nintendo had definitive evidence to suggest the Atmosphere devs are profiting off of piracy, they'd do the same thing in a heartbeat. Same with Ryujinx, Luma3ds, or any other form of emulation/homebrew. The only reason they don't is because they know only way they'd stand a chance in court is if they make it about piracy, copyright protection, and stolen profits.
Ngl Windows is more annoying to install than Linux Mint or Ubuntu. The average user can just click through most of the default settings just fine unless you're trying to have a fancy dual boot setup