A few thoughts:
- Just realized that deactivating layers is the same as using the OAM viewer. Apparently you can't use keys to deactivate the layers.
- Btw, No$GBA is another emulator that comes to mind, never used it though so I can't say if it's better for ripping.
- Also I'm not sure if desmume can deactivate or separate sprites on other sprites.
- I also tried changing the palette colours like I can do in vSNES (black to pink), but as far as I can see, that's not possible with desmume.
I also took a look inside the sections and saw that a lot sheets have been done by Ragey.
He probably used GGD for his YI / SPP tile rips, since he states the colours inside desmume tile viewer are slightly off (not sure if this is an issue anymore after all these years and updates, I haven't checked it):
https://randomhoohaas.flyingomelette.com/ai/spriterip/
Anyway, my knowledge about DS ripping is too limited to really help out, all I can do is pointing out methods, links, emulators and tools. If I would decide to try ripping DS games, I would probably download everything related to this topic and try around like a little child with a box full of toys (does tool/method/emulator x works well with game y?).
In the end, all you can do is trying around with the stuff you can get your hands on.