I do not know much about your first question, but when the pH becomes acidic, below 7.0, the beneficial bacteria in our filters go into a dormant state.
At a pH of 6.6, the bacteria start to drastically slow down the processing of ammonia and nitrite, and anything below that level of pH the bacteria will become dormant, and the bacteria will not process any of the two toxins in the water.
I never heard about ammonia changing to ammonium when the pH becomes acidic, someone else will have to answer that for you. But based on what I know, I would say that the bacteria will not process ammonium. I think by the time ammonia does change over to ammonium (if it does?) that the bacteria will already be in a dormant state.
As for the ceramic media in your filter, you do not change that out.
That is where your beneficial will colonize the most. The only time you would every replace it is if it was some how falling apart, and it could not support the bacteria efficiently.
-FHM