Just to give this discussion a bit more perspective....
Given what we know about what happened in Japan, I'd say that Nintendo isn't only worried about the potential of pedo's using the 3DS to groom children. They're also worried about something that most of us in the west probably wouldn't even consider, namely that underage girls might be using 3DS messages to actively solicit sugar daddies for enjo kōsai ("compensated dating"). Though most enjo kōsai apparently does not result in sex, surveys in the past have suggested that as many as 20% of schoolgirls in Japan were engaged in the practice.
Now, we don't know for certain that the cases which prompted this reaction from Nintendo involved enjo kōsai. But the possibility is something that'd occur to people in Japan, and it should be something that we take into consideration when evaluating the appropriateness of Nintendo's actions. In a household where the parents are doing everything right, with their computer in a public room and the child's phone usage monitored appropriately (which can be done without invading the child's privacy just by checking the numbers of messages against the bill, and making the child aware they're not to delete anything), the 3DS is easily a weak link in the armour. It's much harder for the parents to track what the children are doing on the device, if it even occurred to them that they'd need to keep track of it in the first place. Not to mention the possibility of the children bypassing the parental controls as well. If the kids can do that, they're probably not stupid, and are reactivating it every time to make sure the parents don't see anything even if they did check.
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