I've already made an attempt at a GBA emulator but it's on hold for now unfortunately. The main issue is that in ninjhax's current form it's impossible to set RAM executable, which means that we'll have to use interpretation over dynamic recompilation (AKA extremely slow). I implemented an ARM core which can only add and it goes dead slow, probably around 1/32 or 1/64th of a GBA's normal speed. Once smea releases an update to allow manipulation of RAM pages (in terms of setting executable or not) I can *maybe* see a GBA emulator coming out.
And for right now, a cheat app is impossible without kernel access. I'm not sure if you've noticed, but if you unplug that Cubic Ninja cart you have it'll kinda stop the homebrew launcher. And you can't leave the game normally either. Better internet browser maybe but flash definitely isn't going to be there. And there is no way possible you could just "convert cia/3ds/etc to 3dsx". 3dsx is designed to be extremely portable, cia and 3ds are not (as much). With GW's exploit coming up a lot of the 3DS hackers will definitely be diving in and doing things, but the chances of this stuff happening within the current Cubic Ninja exploit or even withing the .3dsx file format is very slim. Heck, .3dsx can't even handle shared libraries, which are used a ton in .3ds files iirc.