Interesting approach, exactly what I had in mind as its better than patching each game. Question is can @Sono or another dev think of a way to implement this?
Are the DS and GBA sides of the 3DS totally sandboxed? What I'm thinking is would it be better (possible?) to run OAF hooked into DS mode for more resources available ala Adrenaline on Vita?
It's not sandboxed, it's the real deal. It's a real DSi, real DSLite, real GBA, under the hood. If it works on real hardware, it works on 3DS as well.
In fact, the way GBA audio is done on the 3DS is probably slightly worse than a real GBA, although on the 3DS you have editable audio filters, so I don't really know which is the better way.
In whatever case, patches need to be done as if you had access to a flashcart on a real GBA.
As for DS, I don't think DS needs this patch? Pretty sure DS has like 16 hardware PCM playback channels (with interpolation support as well?), so it should be already as good as it would get.
Although in case of the DS, it is possible to get better quality mixing via emulator enchancement, but that's sadly not something we can achieve on the 3DS due to the way GBA audio is tacked on.