Why wouldn't somebody want to use the cooler that cools the most all the time?
TL;DRThe strongest cooler isn't always best because of trade-offs between emissions, safety, cost, weight and power draw, plus higher repair and replacement costs, as with industrially tuned components that have larger signature multipliers.
Similar reasons, really, just on the opposite side of the spectrum, where the power plants are dealing with EM and coolers are dealing with IR. It's sort of a balance between emissions, safety, cost, weight, all these things. You can disperse a ton of heat, but you're possibly drawing more power to do so. These things don't necessarily scale one to one.
And since you are cooling better, you are generating more heat by the component.
For a live in-game example of this with the cooler, I want to say it's the Aurora CL. It has more industrially tuned components, so it's going to have a higher baseline power output and a bit more cooling efficiency, but in the same regard, they do have much higher signature multipliers. So you get that benefit, but it's at the cost of, well, if you're a cargo ship, you aren't really caring as much about having a baby EM or IR signature. You're caring more about 'I want to move this cargo from point A to point B.' And so it's sort of that trade-off you make.
Also, there's damage to consider. When you're in battle, repairing a component that is more costly, larger and more beneficial requires more resources. If it actually gets destroyed, having spare parts for repairing that component will come at a greater cost.