Why do pilot and GPWS approach callouts say “minimums” instead of “minima”?
Minimums is an acceptable plural of Minimum (along with minima). 

As for why its used as a call out is likely because it is the preferred pluralization used by the FAA and in my experience the term generally used when talking about "approach minimums" or "weather minimums". 

Its worth noting that the FAA uses both minima and minimums in their handbook.