I could see someone making a WiiScrubber-style program that can edit 3DS files (like the Wii ISOs) and release groups would just remove updates before releasing the games. No more accidental updates for pirates. Every access point within my Wireless-N card's reach is passworded so randomly connecting to open Wi-Fi won't be a problem at home for me.
If the automatic updates via the Internet can't be disabled then someone will (eventually) come up with custom firmware that, at the very least, has the automatic update portion removed or disabled.