Not sure about 9.3+ FW users on non exploitable consoles (they are pretty much stuck with using Hans. It will be the only way), but when I'm getting my n3DS, it will be on exploitable firmware so I plan on simply repacking my games with the cpu speed enabled directly in the exheader. If you look at 3dbrew, it tells you the flag that sets this and where it's located. "00" means standard o3DS speed. 02 = n3DS speeds. 03 = n3DS speeds plus L2 cache enabled. (whatever that means.
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You find this setting at offset 0x200 at 0x0C on the exHeader . SSB has it set to 03 for example. I guess L2 Cache enables extra memory (and thus the reboot on o3DS to enable the expanded memory)
You may be able to edit the exheader directly by editing the CXI it's in instead of unpacking the game's exheader and other files (this would save you the trouble of repacking the CXI correctly).
In that case you'll find it at 0x400 offset instead (still at 0x0C). Note that you'll need to fix the hash for exheader in the CXI header afterwords. I just use Decrypt9WIP by d0k3 to retail encrypt it. This fixes the hashes automatically during the process and found it to be a quick way of editing this value.
I plan on repacking Ocarina of Time as a test. (as I hear this has sound bugs with the higher speed. When enabled through Hans anyways)
I may also see if I can just create dummy patches that enable it instead of repacking an entire game.
Aside from that, Hans will be the only other way. I can't know for sure I can repack games to use n3DS clock speeds until I got an n3DS to test on. But others are free to try it in the mean time if ya'll know how to repack a game CXI correctly and are savvy with a hex editor.