If you are using AuReiNand then I have an idea that just might work.
Any homebrew that you can install as CIA do so. mGBA can be installed as a CIA and works better that way if I recall correctly.
Also, take advantage of the Payload feature of AuReiNand. Your arm9 brew such as Uncart and Decrypt9 and such can be launched as soon as the 3DS is powered on.
In the Aurei folder make a folder called Payloads. In this folder place the .bin files in here named as such in the picture below.
View attachment 45433
You must have a default.bin which is why I have two instances of Decryot9. It is just easier to turn the system on while holding a direction on the D-Pad.
These payloads can be launched by holding the corresponding button while powering on your 3DS. Again, mine use the D-Pad as it is easier to push while turning on the system.