I think it has something to do with the H+ ions disrupting proton ATPase, and secondary active transport, but I only have a fuzzy (at best) understanding of microbiology.
It will do that, yes. It will have a lot of affects really, it depends on how low the pH is and where you want to look. If the cells are having trouble maintaining pH homeostasis, you’ll end up with non-functioning enzymes in many instances. The individual amino acids in the proteins become protonated (in a pKa dependent way), which can affect structure and function.