Aquaponics is about managing waste within the system rather than flushing them back into the natural environment.
I live in the driest city in the world, we're on the coast, and other than a couple of power stations and aquaculture companies I'm not aware that any other industries use sea water.
If they could make use of seawater as industrial process water I'm sure they would!
There are some remote mine sites that use "mine water" which is basically groundwater seeping into where they're digging as process water. On some of these sites this water is very saline, and it needs to be taken into account when designing their process systems. They only use it because there is no other option for water supply.
I used to do a bit of work at a mine that would have had about 150 people living on site - they work for a few weeks then fly home to their families. They were having to bring water in via trucks to supply the camp. They had 2 trucks, each with 3 trailers, and the water source was about 200km away. They looked like this but with another trailer.
I've always thought that there is potential to get fresh water from power stations where they use sea water in their process. Just need to catch and consense the steam...