Nintendo probably learnt from the last time they tried pulling shit like this on the Wii to remove the Homebrew channel (which also ended up bricking people's Wiis, Homebrew'd and non-Homebrew'd alike).
They also can't access the SD card (legally) to pull something like this off as a user could easily just set their SD card (especially the case of O3Ds SD cards with a physical lock) to "read only" so any Payload they'd like to put onto the SDcard, and launch on boot would fail because they wouldn't have write permissions to the SD card in the first place.
There's really no inconceivable way they could pull something off to remove A9LH. We're just too "close to the metal" for them to do anything. We're in their system before even their own OS loads/boots, so we get the first punch as it were (meaning we could patch certain patched sys calls etc before their OS has time to even load them (great example is the SVC backdoor they patched on 11.X, and in the same day - Luma had a patch which re-enabled it)).
They're most likely concentrating on the Switch, more than the 3DS at this point (to prevent a repeat of the 3DS modding scene most likely) but lets not forget, A9LH came about due to Nintendo making their boot sequence overly complicated, and thus - created loopholes due to how complicated it became. If they do the same with the Switch, expect A9LH-like exploits mid way through the Switch's lifetime due to bad program design decisions.
