Hi,
as Prince said the two religions play minor roles and are there for the sake of historical accuracy/plausibility. The problem with both of them is that since no faction is of the jewish/heretic religion their percentages can never go up - neither naturally return to the jewish/heretic religion because no province is designated as jewish/heretic inherently (unlike others that are designated as catholic/muslim/orthodox). However there are plenty of hardcoded events that affect the heretic ratings in certain provinces, like for example the Cathars in Toulouse in the course of teh game. These give high boosts of the heretics in the said provinces (iirc in Toulouse heretics become more than 5%?). These can be fought back with the use of inquisitors (if you are catholic) or ulamas (if muslim) and iirc cannot be fought back if you are orthodox (or pagan).

However the game can be modded in ways that these are not "lost" completely - for example a jewish faction could be introduced (like the Khazar Khaganate) or, like the Pocket Mod had tried to do some years ago make spies spread heresy wherever they go.