On the Wii, modchips existed before any keys were known. It was thanks to modchips that the first ever custom code was run on a Wii (GC homebrew). On the Wii, all the first modchips did was make the disc drive accept burnt discs. As the burnt games were direct copies of legitimate games, all the encryption and signatures were in tact, so the games booted. The modchip just told the drive to accept the disc. (GC discs didn't have the same cryptography applied to them, so once burnt discs were accepted, it was fairly easy to load a custom GC disc with homebrew on it, which allowed Team Twiizers to poke about in memory, which led to the Twiizer Attack and eventually to the discovery of the Trucha Bug, which then allowed them to create custom Wii discs and load them using modchips)Do you need the encryption of the device to make a modchip? *** Don't flame me. I don't know much about this subject***
EDIT: So in theory perhaps, a modchip could allow a flashcard with an exact 1:1 dump of a 3DS game. Although if you clone the hardware of a 3DS card, it shouldn't be necessary to use a modchip.
In short, a modchip will probably be no use on the 3DS. They are really more for disc based consoles.