There are well-established plans, protocols and procedures for vulnerability disclosure and exploit development in the 3DS hacking community.
It was a surprise that Nintendo reacted so quickly and fervently with regards to Freakyforms/Freakyhax, but then again, the community had acted in like; it was widely disclosed and well-documented on the moment of its release.
Freakyforms does nothing on 11.0 that OoT can't do on 11.0, and it does nothing on 10.x and older, that Cubic Ninja, Browserhax, et al, couldn't do before.
Nintendo could Ironfall Freakyforms, too - plug the hole in a software update, and make 11.1 not launch it without an update.
Some suspect Nintendo is even watching other 3DS hacking and homebrew communities, too.