Would be nice if it could be done via a Home Menu hack liked Region Free but doesn't seem likely.
On "that" ISO site there are patch files for games that will enable the N3DS Clock Speed but since patches are region tied kinda screwed out of using them unless got the right version.
At the same time though does N3DS Clock Speed break something like Multiplayer? the other day I was trying Pokemon local and got a connection drop error didn't occur to me right away but I had NTR running, is it just an NTR issue? I don't believe I had told Pokemon to run at N3DS speeds, does NTR remember per game if you have set it during that consoles on time? always keep mine in sleep.