There's a few lines here that need to be drawn somewhere. Nintendo sells access to a platform to developers. It's not unreasonable that they aren't allowed free reign to control what's run; at some point one developers free reign would conflict with anothers.
Should the consumer have free control over what's running on their hardware? Perhaps. Let's for the sake of argument assume yes.
Then how should Nintendo and third party developers deal with hackers? Completely cut their access to Nintendo/game services? Now they have a brick.
The lines drawn for developers and consumers with respect to game consoles make sense and generally work for all involved.
I think your point has legs in other contexts (i.e. Apple products, right to repair, etc) just not here. If people feel differently they should vote with their dollars, but managed walled gardens will always be greener in some aspects.