Right, I myself was wondering about not being able to disable the bottom screen on the 2DS anymore. It works for sure on 3DS models, but I know that it wasn't the case anymore with the 2DS following the new working builds (i.e. the post screen tear fix ones).
I have a 2DS as well, I can test it. I'll edit once I do.
Edit: Okay what the heck. I guess i need to reset the config on my N3DS but it works way better on 2DS (The menu is actually smooth in XMB, scanning actually works & doesn't crash)
Anyway to answer your question, I can't turn off the bottom screen either with the 2DS. Only with my N3DS I can.
Edit 2: Okay I reset my config for my N3DS - still can't scan anything. Scanning worked out-of-the-box for my 2DS. What gives?
Edit 3: This is confusing.. scanning works great now & I can launch the "Retroarch" app without it saying "the sd card has been removed". All I did was the new system update, but I don't think that would let it work. Oh well, at least it works. Also it seems that the XMB menu isn't as smooth if you have a video filter applied. Also, sometimes while in game, if you go to the home menu & back the sound won't work until you restart the emulator.