Very cool read! I learned a lot. Let me quote a few interesting passages.

Fish do congregate around wrecks and make them their new homes, but (emphasis mine):

Paxton, Taylor and their colleagues are working to further understand how fish use artificial reefs, and if new human-made reefs prompt fish populations to grow or just pull them from elsewhere. “Are these fish being taken away from nearby natural habitats, or over time are new fish actually being produced?”

Not to mention pollution potential, even from basic building materials like iron that persist after intentional scrubbing and decontamination:

Almost anything can become a reef under the right environmental conditions. But many objects can be sources of underwater pollution in their original states. Toxic paints, asbestos, iron and rusting metal particles can seep out of the structure and into the surrounding waters. Because of this, official reef-creation projects include extensive cleaning and decontamination before the structure or object is sunk into place. That’s not possible, of course, in the case of shipwrecks, which often sink and are abandoned in times of duress or bad weather and only are rediscovered as artificial reefs years later.

For example, scientists have noted instances of iron leaching from sunken ships and having adverse knock-on effects on surrounding reef life. In 2008 at Palmyra Atoll, a reef formation and U.S. National Wildlife Refuge south of Hawaii, researchers observed an invasion of a type of sea anemone called a corallimorph around a shipwreck. The vessel, which ran aground in 1991, was moored to the ocean floor by iron chains. Algae need iron to grow, but the element isn’t plentifully available in many parts of the central and south Pacific Ocean, so its sudden abundance prompted an explosion of algae and an unbalanced invasion of the corallimorphs. The overgrowth, dubbed a “black reef” by scientists due to the anemones’ dark coloration, stretched for over half a mile around the shipwreck and smothered the existing coral in the area. 

Invasive corallimorphs, a type of sea anemone, crowd out coral around a shipwreck site at the Palmyra Atoll National Wildlife Refuge in the central Pacific Ocean. (Thierry Work, USGS)

The shipwreck was removed in a multimillion-dollar restoration project spearheaded by the U.S. Fish and Wildlife Service in 2013. In the years since, scientists have had some success with attempts to rid the reef of lingering corallimorphs with pulverized bleach, a treatment that could be used at other similar sites. The Palmyra Atoll is renowned for its biodiversity (it’s home to three times as many coral species as the Hawaiian Islands), and scientists hope the restoration and removal efforts will help retain the area’s abundant marine life.

So, it sounds like these wrecks can become habitats, but they aren't as biodiverse as natural coral reefs and can have other negative consequences. If we've destroyed the natural habitat, then these can be band-aid replacements so the fish at least have somewhere to go. If the natural habitat still exists in an area, then that natural habitat is much healthier without contamination.

On the one hand yes. But, and this is a big but, typically when ships are sunk by the government, a lot of environmental impact studies and decontamination processes are preformed. The goal is usually to create artificial reefs, which is pretty useful because of how much damage we’ve done to the natural habitats.

Does it balance out, or make up for it? I don’t know, I’m not smart enough. But I do know the artificial reef projects are greatly appreciated and highly desired by local governments.

Yeah, but it's not "profitable".

If you think the paint contamination after decommissioning is bad, just wait 'til you find out about how antifouling bottom paint (whether hard copper-based or ablative) works during the service life of the ship, by design.