Since there are two questions to be answered here:
1. Can the MSET exploit be used on N3DS? Sure, just downgrade the MSET app to the one from 4.x, and then you can run Gateway or whatever other CFW if you're on 8.1-9.2.
2. Can you run Sudokuhax and/or inject other DSiWare stuff over the DS Internet Communication app on N3DS too? Yes, make a backup of your sysNAND (or emu if that's where you intend on trying it from), use Decrypt9 to dump your TWL_NAND partition and use a program to mount it as a FAT16 image, then replace the proper app (I forget its title ID off the top of my head, sorry), and re-inject it into your sysNAND's (or emuNAND) TWL_NAND partition.
Sudokuhax is handy for reinjecting the profile exploit without needing to use a flash cart.