I thought they tend to pipe far out and discharge as far below the surface as possible, since there is a lot of surface life and it is less damaging this way.
Ships (with long submerged pipes) would be prone to weather events and generally less reliable than an installed pipe. Perforation would be prone to clogging from build up so a nonstarter I would expect. Adding flex tubing and a relocation robot would be a maintenance headache as well. Not sure there is an easy optimization.
Ships wouldn't need a long submerged pipe. It'd just need a small hole like a bilge drain or maybe a live well on a fishing boat. Just let the boat cruise around slowly draining back into the ocean.
As for surface life, I'm no oceanographer, but is that really the most vulnerable place? The surface is where fresh water rain meets the ocean, so that would dilute the salinity during storms. However, there's nothing to say that another pump couldn't be pulling from the ocean and mixing the brine into that so it's diluted before and not just pouring brine straight into the ocean