Speaking as someone who has managed to get Unity CIAs working on a retail 3DS, I can hopefully give you a brief method, that I often use, which could perhaps work out for you.
1) Download the latest 3DS Simple CIA Converter (an easy-to-use program which handles zero-key-encrypted CIAs) and place your output CCI file inside the "roms" folder.
2) Rename the CCI extension of your file to .3DS as the program only detects files with that extension.
3) Open the program and choose the option to convert 3DS to CIA. Let it do its business, and after a few seconds, the file should now be converted to a CIA, ready to be installed to your 3DS.
4) Finally, send it on over to your 3DS and install via your preferred CIA installer.
The result varies from 3DS to 3DS, most likely depending on your setup (I personally use A9LH + Luma3DS hourly) but I have always found this method of converting and trying out a Unity CIA has always 100% worked out for me!
I also forgot to mention that you shouldn't have ticked any of the boxes in the Build Settings (development CCI and convert to CIA image boxes), as they can also render the CIA unplayable.