It is sales and public perception. Nintendo has enough bad press right now with all the talk of how the Wii U is failing. The situation is much different with the 3DS obviously but what happens if there is a sudden media blow-up of children being tricked into child porn with the system. How many parents who won't have bothered to look into the system and how it works suddenly react? Will parents want to buy the system for their kids with this shadow threat of perverts being able to somehow reach out to their children with this device? Will parents who already have it for their kids suddenly want to sell the system fearing it is a hazard?
Nintendo has said the family market is a big focus of their business. While enthusiasts like ourselves know and understand how the system works, it is still stunning the amount of people who have no idea about anything game related. Just last night, I was in an EB Games (Canadian Gamestop) just browsing a bit when a call came in. One of the clerks answered and was talking to the person on the line. He went over to the Wii U section of games to find a game for the customer. The customer was looking for the Wii U version of Minecraft. The clerk couldn't find it and then asked the other clerk if they had any copies. At least the second clerk knew his stuff and said it wasn't released on the Wii U or nor was there any announcement made it was coming to the Wii U and not to expect it to happen.
This is in a shop that specializes in video games and not a Sears or Shoppers Drug Mart where it could be a bit understandable that the people working there might not be too familiar with all the different games available on each system. This is where you expect people to be knowledgeable about such products. Clearly that isn't the case either. So, it is not too surprising that rather than endure some potentially bad press and have to educate consumers as to how the technology actually works and point out that lax parenting is to blame, it is easier to just disable the application right now and figure out a new solution going forward.
The media is always looking for a scandal to sell papers or get viewers. A local TV station tried to make a big thing out of Pictochat once which some of you may remember when we derided it on this site. That's the desperation of today's media to try and find something that catches the publc's attention and they can milk for awhile. Unlike the Pictochat "scandal" that was laughable due to the limitations of Pictochat's technology, a Swapnote scandal is something that could be taken more seriously because this could be done worldwide and such trouble is, and obviously was, able to occur.
Finally, while some people have outcried this as a horrible loss and that they loved the feature, I wonder if that is true with the majority. With the Wii, I know Nintendo would ask about being able to track the system's usage. I forget if the 3DS asked me the same thing but I think it did. Regardless, it wouldn't surprise me if Nintedo was tracking every system's usage it could. If so, I expect they may have seen that the use of Swapnote had fallen quite sharply from when it was first introduced. Getting new stationary was a huge thing for awhile but it slowed down more and more. The reason may be because there was less and less interest. Thus, they may have looked at the usage and figured disabling it would be the best solution. They probably expected some negative feedback but that the majority would be indifferent to losing something they had stopped using a long time ago.