From a business perspective, the only reason would be to keep their customers happy. The n2DS XL was discontinued a little over a year ago and people would get mad if the online services were shut down while the 3DS/2DS was still a popular line of handhelds. As long as people are still playing 2DS/3DS, they might still be buying new games, shutting the online services down would lose them some game sales.
As more people get a Switch (or another console for that matter) and stop playing their 3DS/2DS there will be a point where the player count is so low that keeping the online services up just for them doesn't make sense.
I think they're just waiting for that moment right now. They put the code into the update so they are ready to pull the killswitch at the exact right moment.
Who knows what the current 3DS/2DS player base looks like, but it has been a very successful line of handhelds and there is a large backlog of games for anybody who picked up a 3DS or 2DS late in its life cycle that they might still be getting through.
