If there was to be one, it would have to reside in the system OS and not as homebrew. As far as I can tell, the 3DS can not boot two different apps at the same time. It can run certain system apps while a game is suspended, but certianly not two games at once (since Ninjhax resides in game user space so Cubic Ninja has to boot up and take up CPU/Ram space to use Ninjhax stuff)
I don't think the 3DS has enough power to record video of a screen while a game is playing. Especially with RAM/CPU intensive games like Super Smash Bros or Pokemon X/Y/ORAS.
The New3DS might handle it to some degree perhaps if you limited it to one screen at a time, but I don't see it ever happening with both screens at once. This isn't even factoring in audio. Though you can just hook the 3DS up to the line in jack of your PC and record the audio that way. It's just a matter of taking the video and syncing it to the audio track in post processing using the PC/MAC program of your choice.
I only see this happening on a Gateway exploited console. Ninjhax is definitely out of the question here.