Yes. But I'd recommend installing Cubic Ninja on Sysnand and running Gateway from there. Why? Read mini-tutorial ahead.
1. Get latest Reinand and ROP Installer (If you don't have a DS flashcart, you can use FBI to install the MSET exploit).
2. Boot on Sysnand using Reinand by pressing B+Start at the "Press start to boot" screen when booting Reinand.
3. Use FBI or whatever you want to install a Cubic Ninja .cia.
4. Boot CN and install the Gateway exploit.
5. Install your GBA games and DSiware TO SYSNAND ONLY.
6. Now you can use Reinand on your 3ds Sysnand to play GBA and DSiware, while using the Cubic Ninja .cia to boot into Gateway.
In conclusion it should be something like this.
Cubic Ninja->Gateway
OG Sysnand->Rei Sysnand↕Gba/Dsiware Games
I also recommend making the MSET stick, so that you don't lose it when playing DSiware games. You can always change the MSET later by using a DS flashcart or FBI if you so desire.
To make MSET stick:
1) Install the exploit using the N3DS_ROPInstaller.nds; e.g. Profile Name: slslasher
2) Launch a DS game, exploit would be gone
3) Go to settings and change Profile Name to another one; e.g. Profile Name: slslasher01
4) Install the exploit using the N3DS_ROPInstaller.nds again and it should be stuck.
Extra Steps because I want to change back my original profile name
5) Go to settings and change Profile Name to my original one; e.g. Profile Name: slslasher
6) Launch exploit and test, there should be an error.
7) Install the exploit using the N3DS_ROPInstaller.nds again and it should be stuck
