Well, yes!
A regular (as opposed to DSi or GBA) CIA or a CCI (aka .3ds) contain some partitions (application, O3DS update, N3DS update, manual, multiboot application...)
CXI and CFA are types of individual partitions, so when you want to hack a 3ds/cia, you actually normally extract partition 0, edit the contents, and create a new archive containing only this one!