I'm not sure about pairing inside games as they use Nintendo's official libraries. I don't think permanent pairing works inside homebrew, though. Paired Bluetooth is stored in SYSCONF in NAND and I don't believe any homebrew I've seen writes to that.
If you want to make sure that stuff running in EmuNAND on GX has the same pairing data then go to the Features settings and click "Copy SYSCONF to EmuNAND" after you've paired your controllers from the system menu.