@Jykzz, if you have CTRNAND Luma3DS, try booting the 3DS without SD card. Hold the (SELECT) button when you turn on the system to access
Luma3DS configuration. Insert the SD card while it's on Luma3DS configuration. Press (START) and hold (START) to access
Luma3DS chainloader. Boot to GodMode9 and check if the
[0:] SDCARD () and
[A:] SYSNAND SD drives are there.
This would check if the SD card reader works at all.
Edit - Nvm. This won't work as CTRNAND Luma3DS doesn't load FIRM payloads from the SD card. You can check if you had GodMode9 put at
[1:] SYSNAND CTRNAND/rw/luma/payloads/GodMode9.firm