Actually, I believe the region encoding is merely programming. I'm not an expert with this stuff, so I don't know the proper terms, but I do know it isn't contained in a specialized chip. Without hacking the firmware (apparently) or swapping out the motherboard, the region encoding won't be able to be changed.
If you're willing, and have the tools and know-how, you could probably just swap the motherboards of a Japanese 3DS with that of any other region's. I can't swear it'll work, but I did the very same with my old DSi. Like the 3DS, it's region locked too. It works just fine. Plus, you get to keep any previously installed software and whatnot.