Here it is :
Apparently, it's to prevent hacks (initial program loader is modified).
Source : FCC (via Myce)
An FCC filing reveals Nintendo has changed the CPU of the Nintendo 2DS to improve the security of the device. The change is most likely to prevent installation of illegal / homebrew software.
The filing talks about the Nintendo FTR-001 which is the Nintendo 2DS as this page on the Nintendo website reveals. In the filing Nintendo reports, “The difference between FTR-001 and FTR-001(-01) is from CPU with a different security function of the initial program loader that is installed in each model .
Apparently, it's to prevent hacks (initial program loader is modified).
Source : FCC (via Myce)