If playing on the (PC or Android), updates are installed directly through the emulator menu: Open Citra and select "File" → "Install CIA" .
You cannot simply drag a .cia file onto an SD card. You need a hacked 3DS. Here is the checklist: pokemon omega ruby update 14 cia download install
If you are using a 3DS with custom firmware (CFW) like Luma3DS, you can install the update as a .cia file using the title manager: If playing on the (PC or Android), updates