Sorry, took time to research about the 003 error bricks (it'd help if you included wii, since '3ds 003 bricks' didn't help me at all...). It's about the Wii, no wonder I was unaware about it. lol
So, apparently, Korean Wii's that installed another region's OS (via hacking, I assume) that is higher than 4.2, gets bricked? This was caused by a mismatch due to a software modification to the Wii; point being, nobody has proof that this was done on purpose by Nintendo solely to brick. The mismatch was caused by the hack, making the owner (who modded the wii) responsible.
In the case of flashcarts on 3ds, there's no alteration in software, meaning there can't be any mismatch in important system files. The only way a brick can result on a 3ds, due to flashcarts, would be a check that would brick the 3ds if a flashcart has been run. On this case, Nintendo is responsible, since it was intended to brick.
Sorry, I'm really no Wii/tech geek, so I'm unsure about the terminology used; if there's a mistake in the cause of the 003 error or anything else, I apologize in advance. I'd be grateful if somebody could explain it easier to me (in non-techy terms).