It could work much like Microsoft does with Xbox Live. Nintendo keeps a log of your system and every game you play. They essentially have remote access to your 3DS any time you're near a wireless hotspot. If they see you've been playing pirated software, they shut you down. The only way to overcome that would be to tamper with the operating system and "spoof" the game logs. Problem is, if Nintendo can access your system to check out the game logs, they can surely see if their OS has been tampered with. Big N seems to be clamping down something fierce.
I'm sure there will be a way to disable the wireless radio. BAM, no more big brother. No more online play, either, but thats something I'm willing to sacrifice for piracy.
Well yeah, if you permanently keep your wireless signal off you could bypass it but like you said you'd have to go without any kind of internet interactivity.
Someone's going to find a way to turn off the "hot spot big brother check me out" feature and find a work around. And if not....I'm sure we all wanted a $300 paperweight right???