Tested 3 SMB3 hacks and a Zelda hack. 2 of the SMB3 hacks were ones that had a lot of effort put into them, and the Zelda hack only runs on specific emulators. Note I had sound muted on the 3ds so I don't know about sound.
Super Luigi Bros. 3: Works, though it'd be a surprise if it didn't, as it merely makes Player 1 use Luigi's sprites instead of Mario.
Super Mario Bros. 3mix: Works great, and it even saves the game just fine (tested save feature by switching between ROMs and closing and restarting the emulator, save file remained when returning to game)
Mario Adventure: Works great
Zelda: The Legend of Link: Unfortunately, does not boot, just hangs at a gray screen, but does not freeze the emulator.
Super Luigi Bros. 3: Works, though it'd be a surprise if it didn't, as it merely makes Player 1 use Luigi's sprites instead of Mario.
Super Mario Bros. 3mix: Works great, and it even saves the game just fine (tested save feature by switching between ROMs and closing and restarting the emulator, save file remained when returning to game)
Mario Adventure: Works great
Zelda: The Legend of Link: Unfortunately, does not boot, just hangs at a gray screen, but does not freeze the emulator.