But for now it is unclear whether Nestopia will use split or joined images.
For romsets, it will use whatever the XML tells it to. Consider the following:
1) <prg size="32k" file="combined.rom" ... />
2) <prg id="0" size="16k" file="first.rom" ... />
<prg id="1" size="16k" file="second.rom" ... />
Same end result for an emulator but (2) is more informational (provided they're in fact two distinct chips) and sometimes even necessary if they differ in some ways, like in the case of two WRAM chips where a battery is connected to one but not the other. PRG and CHR will always be treated as two separate entities, meaning each element will point to a different file of choice.
For databases, the source image file can simply be of any type. Standard CRC32+SHA1 lookup of combined PRG+CHR data will be used to find an entry.
As for ROM file naming conventions, I honestly don't know what I like best. xxx.prg/chr? xxx.bin? xxx.rom? xxx? Since it's outside the scope of the format anyway I think I'll just stay out of that one.