My understanding is that our 24v motors/pumps (all of them, not just the ones on the watermaker) should have their negative go straight to the battery bank. The bonding wire should be connected to their cases.
Have you noticed any change in how fast your zincs erode? If the watermaker is properly bonded, the zincs should protect it.
If there is a connection from positive or negative to the case within a pump, usually caused by wear of the brushes and buildup of carbon dust, you can get electrolysis anywhere in the circuit. I would disconnect your pumps one at a time and check for a connection (use multimeter on resistance) between the positive or negative and the case. If you find a connection, find the cause. Before you hook everything back up, check for connection again between battery negative or positive and the bonding system, in case there are more than one places where there is an unwanted connection.
Let us know what you find.