Is local multiplayer communication fast enough to enable parallel processing?
I guess it could work and it would be fast-ish. The communication between the systems would have to be fast for smoother multiplayer gameplay anyways but I'm not sure how much SB slows it down if it does. You can try it though. To allow more than four systems though you'll have to do some multiplayer switching which requires manual input so the system couldn't get bigger for it to be automatic. You can use audio to transmit information like Petitmodem but it's far slower than the standard multiplayer communication method.
I do want to try this idea, but it needs a good program concept to go along with it. I was thinking of maybe a platformer which sends all physics/AI calculations to the other 3DS and only renders graphics. Or a board game AI that evenly splits its tree search between two 3DS systems. I'm going to buy a download of SmileBASIC for my sister, who has an old 3DS. Making a program that sends more time-consuming calculations to the new 3DS and runs the main program on the old 3DS will be a cool thing to try to program!
Try a split-system emulator. You might have to understand low-level hardware stuff such as bitwise operations and assembly and networking to accomplish this but at least you would have made a (programmable?) cluster machine. That's probably one better than the emulator I'm planning.
But a game like you suggested would work quite well and could allow sound-networked games up to as many connected players the server 3ds can support without lag. Of course for that you'll need audio cables which support the 3ds audio jacks and something to merge and process the signals for the server 3ds. For now two 3ds systems and a compatible cable cut in half and rewired the right way to allow bidirectional communication can probably work. Starmade multiplayer works like you described.