GodMode9 is started instead of the Home Menu and will not apply any "live" patches. Luma has no such option as far as I know. But at one point I saw something that goes into that direction (not released yet):Please correct me if I´m wrong but shouldn´t it be possible to dissable the 3d setting via godmode9 or luma?
https://gbatemp.net/threads/important-poll-what-hardware-problem-does-your-3ds-have.519878/