Technically, yes and no. That depends on whether you consider the software provided with the 3DS to be part of the console. If it's argued in court that the software on-console is inseparable from the console, then whatever I do with the hardware is my business. If not, then yes it is circumvention. Anyways, that's for a court to decide.
Once you add a CFW to the mix, the answer is always yes - the signature check is undoubtedly copyright circumvention. Whether that's legal or not is left to the user and the laws of their own country.
Running homebrew only is undoubtedly 100% legal in the US (the portable computing device exemption), whereas in other countries even that may not be legal.