A lot of people with CF take antacids. A number of people have told me that the antacids not only help their stomach problems but they help their lung problems too. This fits with my experience as well: when my stomach is too acid, I have more lung inflammation, more phlegm, and a rough cough.
You can treat excess acidity without drugs if you want. Diet and supplements and some simple home remedies can treat it, without drug side effects. I don't take antacids but I do go to work hard at keeping my acidity under control. It has helped me get off several prescription anti-inflammatory drugs. I no longer take any anti-inflammatory drugs, not even OTC ones. I would highly recommend that you learn more about controlling acidity in your child and work on treating it as early as you can. High dose ibuprofen treatments have been shown to reduce incidence of infection in pwcf because it helps control the inflammation. But acidity is the root cause of most inflammation. People with CF tend to be extremely acid. There are other studies which show that reducing this extreme acidity in pwcf can help combat infection, even infections as serious as PA.
I don't really recommend taking ant-acids. But if you don't know how to treat it using diet and the like, then taking ant-acids is far better than accepting the consequences of doing nothing about "hyperacidification" in pwcf. It is known to promote infection. In my experience, there is a much stronger relationship between gut health and lung health than most people seem to think. Keep her gut healthy and you will almost certainly see less lung damage in the long run. (But you can also cause problems if you make her stomach too alkaline because then she can't digest food properly. This is one of the reasons I am not thrilled with antacids. Alkaline foods and topical treatments for acidity won't cause this issue.)
Good luck.