Vanilla game has no ducks.
Ducks are in both mods, and share the same resource names and stuff for compatibility between mods, so they can be used correctly in production chains, whichever production way you pick.
In CC, the Ducks fly, in RK's mod they don't. The mod loaded on top overwrite the similar files from the mod loaded under.

As they share resource names, you'll either have flying ducks everywhere including in your duck pastures if CC is loaded on top, or walking ducks everywhere including as wild animals on the map if RK's mod is above CC. It's basically just a cosmetic change.

Basically it's not a "problem", and not really something that's likely to change unless either RK or someone at BL decides to change the name of the file for the ducks to have 2 different kinds of animals, while making sure they still give the same duck meat when killed.
Doubt anyone would feel like republishing a whole CC for just that, but as RK is still working on his editor's choice mod, maybe you can convince him to have a look at that. I'd recommend suggesting it on WorldOfBanished.com (RK's site) if it really bothers you.