If freedom of speech gives individuals a license to say anything in any medium, then this means that artificial scarcity is inconsistent with free speech.
If artificial scarcity is immoral, then all information products are immoral.
(Note that as a practical matter I suspect that Nintendo only cares about "hacking" insofar as it undermines sales. I can't see why they would care about people modifying the games or equipment they own. I can totally see why they would care if someone invented an SD card cartridge for the 3DS that allows you to run every game ever written from it. Such a device, if mass produced and sold for profit, is clearly intended for piracy. Moreover, its easy to see how such a device is parasitic on the platform itself, so that if Nintendo didn't do something about it then there won't be a Nintendo.)
If the later is not allowed, this very comment might be illegal, as I'm telling you that such a thing is possible.
Nintendo has previously sued a company for selling a device which allows people to mod the device they owned. https://en.m.wikipedia.org/wiki/Lewis_Galoob_Toys,_Inc._v._N.... Nintendo is notoriously anti-consumer in this regard.
And anyways, restricting mods is unnecessary to encourage the economic viability of video games.
If you can't come up with an argument against that then you're not trying hard enough. The most obvious is that sharing a mod is free speech and ought to be protected as such.
It's also unclear how mods contribute to copyright infringement in any meaningful way. I'm having trouble finding details about exactly what Neimod's mods entailed, but most mods I have experience with require an existing copy of the game.