Well, I just double checked my statement and made a program testing a simple for loop, definitely not something threads could help with, and my 3DSX build was about 2.5 times faster than my CIA build. I can't really imagine anything but a clock speed bump having that effect.I thought they simply added two more cores clocked at 268Mhz.
It makes sense though, the DSi had a speed bump. So why not the new3ds, It's odd that nintendo didn't publicize there system having a clock comparable to the Wii, but then again they never liked hardware specs.