Once added to the buildbot, all 'supported' cores should work. Although PCSX-ReARMed wasn't able to identify the .PBP and .CHD images i tried. I'll add a few cores to my previous post.
Now with regular downloads working, being able to update from the 3ds should be fairly easy to implement.
The .3dsx build just needs to be downloaded and replace the existing .3dsx core.
The .cia builds needs to be downloaded and installed, which retroarch is already capable of.
A few changes are needed on the buildbot side. It needs to offer separate downloads for the cores, like most other platforms already do.
Off course, this still needs to be discussed with the libretro team. But i think it would be a nice feature.
Are you planning to discuss it with the libretro team? It seems like they're happy to get 3DS improvements, and I see questions about missing achievements on 3DS in their chat all the time.