Could the overuse of antacids inhibit protein digestion?

Sure it does... The high acid environment of your stomache, inresponse to food ingestion, is needed to activate some digestive proteins such as enterokinase and tripsynogens (and many others) to help digest the foods u consume. Antacid use is thus not natural and can affect the process of digestion, but some people need antacid to help with pain/ulcers etc...It is compliacted process. Have fun learning.