My unscientific understanding is that this is on balance an environmental good - although that is admittedly based on scuba diving experience, where there is such a visible profusion of marine life once you come upon any reef (be they of the natural or artificial variety).  Perhaps others can comment on the net global cost/benefit.

Remember this attempt to use old tires?

In the end, it all comes down to biodiversity. Poison Darts--Protecting the biodiversity of our world

constructing artificial reefs of limestone, concrete or heavy steel.

I remember reading about successful programs to actually bring coral back to south Florida, I think using concrete.  It seems the subway cars are heavy enough to not get knocked around, according to the NY Times article.  The main problem I see is, the steel will eventually corrode and the disintegrate.