I'm 99% that NINJHAX will work fine from ROM on a Gateway on 9.x as it currently works fine on 4.x consoles.
The last 1% is simply because it's not released yet, so no one can be 100% sure. But it's not likely that the update will break it, as there are a lot of patches applied in GW mode on 4.x (emuNAND or no emuNAND) and it still works fine there. ROMs in GW mode play exactly like real cartridges, with the exception of saving. GW didn't remove or change anything that could break the exploit and I doubt that will change when they release their 9.x update. If anything, the 9.x exploit would be patching even less things as it probably has less access on 9.x, it's quite likely that it just emulates a real cartridge like Sky3DS does but we'll have to wait and see on that part.