1. No, doesn't look likely as of now, since the gba flashcart may always be used as a boot device.
2. I wouldn't think you need to patch homebrews. My understanding is they're usually ds.gba files that are flashcart compatible. The more relevant issue is that homebrew possibly may not be working because of bugs in the current menu (not sure if that's all been resolved for next menu)
3. No, I haven't seen the Canon SD in the compatibility card list, so don't know if that works. Every menu release, though, seems to add more SD cards to the compatibility list.
BruceG