Increasing the CPU clock permanently makes zero sense. Why would Nintendo want this? If it were CPU related, the most sensible would be to be opt-in for newer games, like on the PSP. The average user would't like their battery life to go down all of sudden.
Also, the CPU and GPU have their clocks tied, so you couldn't mess with one without mess the other. Due to the reverse engineering done at 3Dbrew, we know the GPU on the 3DS is accessed through a service, kinda like on a PC, and that the commands are managed by the OS (since the GPU can be used by up to four different processes, which would be impossible if games were accessing it directly).
Keep in mind that reducing overhead for OS calls would actually lessen the load on the CPU while the game is rendering. Once the commands reach the GPU they would take the same time as usual to process, but since the CPU has to wait less, it can resume work while the GPU works in parallel.
Wow, didn't knew that. So, is possible to release a higher spec 3DS with another GPU vendor after all!? Maybe the Wii U is setup in a similar way... that would explain lots of stuff actually.