I don’t know, this sort of thing is a hard one.
One one hand, you have players who are legitimately trying to climb the scoreboard or play fairly or whatever, and on the other side, you have those who would choose not to do that, and instead, cheat their way to the top.
Obviously, some of these users are also some of Nintendo’s biggest fans (since if you’re willing to dedicate the time and effort required to the game in the first place, you are clearly a fan!). Nintendo can’t just say “Meh, cheating” because they risk making their online play a joke and pushing folks away.
I’m an avid GW2 player, and I would stop immediately if ArenaNet didn’t actively work to stop out cheaters who would otherwise wreck the online economy or otherwise affect my enjoyment of the game.
Now, unlike GW2, Nintendo controls the platform, so one of the things they can do is detect modified devices and react accordingly. Of course, they could attempt to detect devices used for cheating somehow, but I’m guessing that would lead to brinksmanship and general cat-and-mouse efforts trying to “detect” the cheaters, so instead they went the other way and banned all the devices from online play instead.
The thing is, these weren’t designed as general purpose devices. They’re “rootable” only through bugs or other modifications that allow them to become general purpose devices. That’s fine - you own the device, you have every right to mess with it, you can turn it into a home automation terminal or drone display or run a webserver on it or whatever you choose - and if Nintendo chose to brick those devices (make them inoperable), I’d have the pitchforks out, too.
But this is more about protecting Nintendo’s online infrastructure from these devices. I wouldn’t want someone with a modified GW2 client to be allowed to connect to ArenaNet’s servers and manipulate the game that way, and would expect them to stop out modified clients as well (and in fact, they do this).
One can argue that instead, they should harden their infrastructure against cheating by reducing the data the client receives and validating it instead (detect when keypresses happen in a way that humans can’t react, etc) - the problem is, I’ve seen this too: back in the days of Everquest, there were several class skills based around “tracking” enemies or users. A MITM tool called “ShowEQ” was designed that would take this hidden data and display it all on a second display that would give you a perfect view of all creatures, their positions, and so on. SOE first tried to deal with this by encrypting the datastream, and when that failed due to grabbing keys from memory, instead crippled all of those abilities by discontinuing that datastream to the clients. Everyone playing those classes suffered from the change, a change caused directly by cheaters.
So, in summary - if Nintendo took a general purpose computing device and locked it down (or required you to lock it down to play a game), I’d complain. If Nintendo disabled the 3DS units in question and made them unable to function if unlocked, I’d complain. But Nintendo choosing to protect their online players from cheaters by rejecting modified clients? I have to be on board with that, and I don’t see that as much a war on general purpose computing as, say, the recent Windows 10 S situation.