3DS Virtual Console
There's two types of VC titles: regular VC titles, and dedicated GBA VC titles.
Regular VC
Regular VC titles: an emulator application + VC ROM in the NCCH RomFS(among other things in the RomFS). The emulator build includes support for all supported VC platforms, not specific to just the included ROM platform.
This emulator includes GBA support, however the GBA emulation for this this is somewhat slow. This was presumably implemented before AGB_FIRM was.
GBA VC
GBA VC is run by AGB_FIRM. RomFS isn't used for GBA VC titles. The NCCH ExeFS contains the same files as a normal application. The ExeFS:/.code contains the GBA VC ROM.