It had a lot of fans wondering what was really going on at the time, as it didn't seem like much of a remaster at all. The Nintendo patch notes provided with this software update stated it "fixed some problems" but as usual, didn't elaborate.
It turns out the story goes a little deeper, with dataminer 'OatmealDome' relaying how the note sharing service actually had a vulnerability in the message parser which was able to be exploited over StreetPass - in turn allowing an "attacker" to run any code they wanted.
The individual behind this discovery 'mrnbayoh' received $1,682 USD from Nintendo (via HackerOne) as a reward. So, there you go - this "likely" explains why Nintendo rolled out an update years after it disabled the app's primary feature.
In case you don't remember, this free service was effectively discontinued back in 2013 when Nintendo found out users were exchanging offensive material. It then disabled the online functionality, limiting it to local wireless.