The TA (MTA) has always had the opinion - 'If we don't need it anymore, there is no need to take care of it unless absolutely necessary".
South Ferry is unique in that a new station was built underneath it. As already stated while the loop station wasn't going to be used when the new station opened the tracks would have to remain in use to be able to turn #5 trains that termineted at Bowling Green (late night and weekends) and to allow for being to switch trains from the 7th Av line to the Lexington Av line (and vice versa) without having the trains go into Brooklyn and then have to come back to Manhattan.
I had always thought that the MTA would keep the old loop station maintained in reasonable condition to have as am immediate back up in case there was a problem at the new station - something that would have been a rare benefit. Obviously the decision makers at the MTA didn't share that thought. So much for the protection of a valuable asset. Because of their way of thinking they had to spend $2 million to get the old station back up for service (and they only did that because of heavy political pressure - they had originally stated they wouldn't reopen the station). I should point out that the old station loop suffered barely any damage from Sandy, which is a testament to the way they built stations back in the early 1900's.
Patrick - in the NYC subway closed/abandoned stations have the lighting reduced to only a few lights for security reasons. There is no reason to keep them fully lit. This is evident in the 91st St station on the #1 line, the 18th St & Worth St stations on the #6 line - periodically some homeless people knock those lights out to make it 100 dark). The Inner loop station at South Ferry still has the original lights going because they use the platform for storage. The northbound Myrtle Av station on the B and Q has lit zoetrope artwork on it and a few other lights but is otherwise dark. The 2 unused island platforms at Hoyt-Schermerhorn on the A & C have minimal lighting but there is plenty of light from the other 2 active platforms. The 9th AV - Lower Level station has minimal lighting for security, construction and crew purposes
There are even different lighting for stations built but never used - Roosevelt Av - lit because it is used for storage, Utica Av - lit and used for storage, South 4th - dark - not easily accessible by anyone so it is not used for storage. City Hall lower level (on the R) has minimal lighting as it is used for mid-day storage of trains and crew purposes.
The original IRT City Hall station is one old station that is kept fully lit - mainly for security reasons. As #6 trains do their loop to the northbound side of Brooklyn Bridge it allows the T/Os to see if there are any unauthorized people there (and the cameras installed work better when there is light).