Tubehax isn't giving the option or running modifications or any unsigned code to be run.The EULA does prohibit the use of modifications or any actions that allow unsigned code to be run, however this only gives Nintendo the right to disable modded consoles. This does not give them the right to take down videos on YouTube. Content on YouTube is not within Nintendo's legal jurisdiction, and them using the BAF to strong-arm YouTube into deleting videos certainly is overboard.
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redirecting DNS has nothing to do with what you said. It isn't illegal to redirect DNS and isn't modifying in any way whatsoever."You may not publish, copy, modify, reverse engineer, lease, rent, decompile, or disassemble any portion of the Software, or bypass, modify, defeat, tamper with, or circumvent any of the functions or protections of your Nintendo 3DS"
tubehax works by redirecting your 3ds connections to a specific dns, which would be considered tampering. o and later in the agreement it states you cant reditrect connections.