This means the arm11 cpu cores are not used at ALL for either DS or GBA modes. The reason why the system menu is disabled when you play a DS or GBA game is because the system has to boot out of 3DS mode so a hacker can't obtain entrance once the security co-processor is busy doing other things (clocking down and working as a DS or GBA processor).
The arm9 core is predominantly used as a security co-processor in 3DS mode which is why 3DS software actually doesn't use the arm9 even though it's sitting in there.
Alright! After some digging I found the answers!
