great question 🥇

FYI - I've never actually heard "denominate" used. It's pretty much always "denomination," which refers to the different types of religions.

Perhaps because it comes from Latin. In Spanish we also have nominar and denominar. The thing is that the "de" doesn't mean "anti" in this case. Nominar is to give name to something for the first time, and denominar, is to give a name to something that already as a name, for other purposes. Let's say you have two chemical samples of the same product, let's say alcohol. "Alcohol" is the "nomination" of the substances, but you can "denominate" the samples as "sample 1" or "sample a" and "sample 2" or "sample b". I think we don't have that problem in Spanish because "anti" is "des". Example: hacer (to do) and deshacer (undo).