Certainly increasing the clock speed of every component in the system would have a consistent effect on all games. But say they only increased the CPU clock, or only the GPU, that would effect each game differently. Some wouldn't gain any noticeable framerate while others would improve drastically. The software theory is very possible, very probable in fact, but I dont think a hardware change can be ruled out. It would be interesting to see a battery life test using the same 3DS and the same game. Three tests before the update and three after (using minimum brightness, no 3D, no wireless and no sound in order to maximise the effect of any extra internal power usage).
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.
