I thought Modern Marvels airs on the History Channel. Anyways, I too saw a show once about the Big Dig. Knowing the MBTA, the doors probably do exist, but are nonfuctional, or they simply don't exist. The doors are probably designed to go over the track, but they don't seal off the area from the top of the track to the floor(the bottom, where the track is attached to, what ever you call it). So if the tunnel does flood, only a small amount can come through at a time.
*edit* Oh darn, Robert beat me to it. Better type faster next time.