When one battery in a circuit runs out, the whole circuit behaves as if it's out of power

From your picture it looks like a problem on the way to you wired your Batteries. Though it should work, the way you connected it the Air Pump looks to only be drawing power from that 1 Battery instead of all 4 might be the problem. Also when it comes to Batteries when it comes to wiring should be only seen as an output for stored power. Having a line come from 1 Battery and input through another Battery is poor wiring design.

I don't know if you can do wiring through a Weaselwort, but I would change the wiring to the top 2 Batteries to come out to the left side through the floor and down the wall to meet with the other wiring in the insulated wall. Then remove the line going to that one Battery to the line going down the wall. If you can't go through the plant have the Battery on the top right's wiring go over the top and down the left wall.