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.