What are those exactly? I don't see similar implemented on the Vita, smartphones, tablets, blah blah...
As for the little comment at the end, it's blatantly not about affordability so please don't pretend that's the case.
Paper trail and law enforcement are the reason, because the 3DS is still regularly marketed at kids. EULA is not actually all that useful in court but a paper trail of where you signed off on removing the content filter most certainly is useful. This is a very common practice for compliance with COPPA. Mojang does it, for reference to a big kid-aligned, company/market.
Credit card charges are one of the main ways to comply with United States COPPA requirements for devices that can be used by minors. If you have issues with it, I suggest contacting your state representative to complain.
For your reading pleasure: http://www.coppa.org/comply.htm Anything that is marketed at children must meet these criteria.