afaik when you run a ds game on the 3ds it simply clears any sort of 3ds code from the ram & cpu (besides the home button code), and it uses whatever resources are available (i wager about 96% available) to run the DS game
so, when a DS game is running, there aren't enough resources available to run the home menu in the background, any streetpass/spotpass programs, any online capabilities (besides the DS ones, but those are deprecated), and all that stuff
but the 3ds system reboots into "DS backwards compatability" mode, so any hacks you have running (e.g. gateway mode) get disabled
unless we can find a way to make the system not reboot when going into ds-mode (afaik a step which can not get removed), we will not get DS games through the home menu