The sounds are stored in a Miles Sound System Compressed file (\steamapps\common\Galactic Civilizations III\Sfx\GC3_SFX_Bank.msscmp). Unlike previous versions of the RAD Game Tools there is no non-commercial/home-use version available.
However it appears that there is mp3/wav/ogg support for mods in the game, but the entire mod-support is not yet active
.
So no changing the SFX sounds as of yet.