Technically, yes. It’s no secret that terrorists have increasingly used cell phones to carry out attacks like the 2004 bombings of a commuter train in Madrid, so it’s only reasonable to assume that once all the stations are wired up, riders will be more vulnerable.
In a New York Times article from 2007, security experts said not to worry, the benefits of riders being able to contact the authorities in the event of an attack, far outweigh the risks. Besides, as mandated by the MTA’s RFP, the company who installs the technology must include a kill switch that could block all calls should the shit hit the fan or as they put it, “under certain security conditions.” Wait, what? Isn’t that the whole purpose of having it in the first place?