Not necessarily.
What they have the right to do is ban you from their services, for ToS violation (running modified software) and possibly make a claim for copyright infringement (using their system software without a license, since you voided yours by violating the ToS.)
What they would not have legal right to do is purposefully brick the console. Remember how Apple got into trouble for doing that with the E35 errors from 3rd party repairs? Yeah, there's consequences of that set of decisions in court, at least for the US. Right of First Sale allows you to do anything you want to the hardware. All Ninty has legal right to do is ban you from their services, and possibly claim copyright violation.