Not necessarily. The digital trunk radios I've worked with can be switched into simple VHF simplex mode. In that case they work just like any ordinary VHF. The firemen would first have to realize that they weren't hitting a digital repeater, then have to switch over. It still might not work all that well in the tunnels. VHF is (more or less) line of sight. In a relatively straight tunnel it would probably work fine. If you were trying to talk to someone around a bend, it probably would not work very well, if at all. Even if you could talk using VHF simplex through the tunnel, you then would not be able to talk to the rest of the reponse team on the surface, who would presumably be working in digital trunk mode. (As I noted up thread trunk mode has many advantages for a big incident.) You might need to have a human "repeater" at the tunnel entrance, with two radios (one VHF simplex and one digital trunk) to relay information.
This is probably what is really required here.

Communication is always a huge issue in any incident. What little I know about radios has been learned the hard way on land SAR operations. Digital trunk systems have many advantages in normal (above ground) operations for a city. But special situations may require special solutions. I'm not sure the fire dept is totally at fault here. It sounds like there is a serious issue of no agency having safety oversight over Metro, with the ability to enforce changes. Given that emergencies have occured in the subways in the past, and will no doubt occur again, planning for robust emergency communication (and testing those plans) seems like a no brainer. METRO should have worked this issue before.

It would be very interesting to learn how other cities with extensive subway systems handle this problem. (New York? London?) I have to believe somebody has found solutions that work.