Maybe they should provide better homes for their livestock and then they would not have disease to begin with nor pest. Medications/herbicides/antibiotics/pesticides in general only have a shelf life of a few decades before resistance sets in. Poor management and using them in the food supply is an arms race with the pathogens/pest.
Better filtration, better environmental recycling are wiser approaches and gets much more effective management out of such medications(you need less and it's more effective).
A healthy place for the liver stock is more ethical, cheaper in the long run and better for the environment.
Intensive aquaculture uses up vast amounts of water resources, can displace and destroy natural wetlands, the nutrient rich effluents can damage adjacent ecosystems.
Sorry, it's not all rosy and the land of milk and honey.
Aquaculture just like Agriculture has the same types of issues.
Agricultural run off is a huge issue for water ways just like aqua culture.
Wise management and mitigation of wastewater via constructed wetlands can provide wetland habitat, waste water purification, reduced cost and impact on natural systems.