The Polo Grounds Shuttle tunnel, or actually the underground portion of the 9th Avenue El, was built upon after it closed. The trackways and tunnels are now the basements for several buildings along 162nd Street. So much for the possibility of a tunnel collapse.
Not quite. Having done the tunnel tour in January 2000, I recall only one "basement" situation - a stairway near the east portal that ran up to what I believe is an abandoned laundry. There are no other entrances into the tunnel from the buildings above.