As to why your dad's old ship & new york sub way cars are being sunk rather than recycled. there's a few considerations, some green, some not so.
Considering your old man's ship first. If it had been a comercial cargo carrier the odds are that it would have been run up a beach in India or Pakistan years ago & would have been scrapped, cut up and recycled that way. As it was a warship "of a certain age" its a bit more murky. The odds are that in its construction specialist (military) steel grades (specifically armour plate) were used in specific parts of its construction. Even although that happened 50 years ago there are still probably some alloying secrets which would be revealed by normal scrapping & that may still be prevented by either government edict or by a commercial contract.
FYI - Modern warships are pretty woossy in comparison to historical warships. WWII design vintage frigates, cruisers & battleships used high strength steel plates up to and heavier than 12" or 300mm thick. Modern ships do use high strength steels, but they are not generally armour plate and are nowhere near as thick. If you get a chance, compare the view along the waterline of say the USS Iowa (WWII Battleship) with say HMS Illustrious (1970's designed Through-Deck Cruiser/ very Light Carrier). On a sunny day, the battleship has a nice smooth waterline look, but on the newer boat, you can see every frame and rib stand out as a high point along the waterline in the reflected light. All this is because the plates used in modern ships are so much thinner (& hence more flexible) than was used even recently.
Secondly, even altough the ship was decommissioned over 10 years ago, the actual layout of the ship may reveal operational specifications of current naval equipment which may be undesirable to give away, on the open market, if the ship were offered for commercial scrapping.
Thirdly, by the time sensitive equipment, ancillary parts and cabling is removed, it may actually be uneconomical to a commercial scrapper to take the ship on as the material that remains may not be economically viable to cut up & recycle.
Similarly with the new york sub way cars, once the motors, cabling & mandatory or easily recycled stuff comes off it might not be economic to recycle the rest.
However, using these redundant vehicles for the creation of artificial reefs has distinct attractions:-
Where there are reefs, fish are able to breed and multiply hence improving commercial and recreational fisheries.
Where there are shallow accessible reefs in diving areas, dive tourism increases.
Where the artificial reefs are composed of semi-familiar objects used in unfamiliar arrangements such as the sub way cars, this has a secondary boost to the dive tourism. There are people sad enough to don rubber head to toe, strap air tanks to their back and spend hours in cold seawater, just to get one of their freinds to take a photgraph of them sitting ina subway car looking as if they are reading a paper. If this opinion offends some, tough, it's actually a quote from my cousin who used to run a dive shool in the Caymans.
Establishing an artificial reef also has benefits in land reclamation as it establishes an offshore hard edge to mitigate erosion of material between the reef and the existing shore.
Finally, an offshore reef has a dramatic effect in reducing the effects of offshore storms on beach front areas, which especially along parts of the US atlantic coast and Gulf of Mexico is a serious concern.
Hope this helps.