Asssuming there are no nanowires, how do I tackle the issue of the biofilm becoming thicker and impeding electron transfer? Is there any method to make the older bacteria detach from the biofilm?
What do you mean by the "electrons from the anolyte"? Are you thinking about electron shuttle molecules? I would say that microbes suspended in the anolyte are not significant contributors to the final electrical output in a conventional MFC, which has activity mainly related to the anodic biofilm.
Geobacter in bioelectrochemical systems grow mainly attached to the anode. Planktonic growth of Geobacter is usually orders of magnitude lower than as biofilm. Geobacter growing as suspended biomass in the anolyte does not have good conditions to release the electrons that could be accumulated due to the metabolism. If the biofilm is thicker, the conditions for releasing electrons would be worst, unless you consider that the biofilm is conductive due to the presence of nanowires.