Why does the zeppelin NT tail use 3 fins?
The likely reason would be ground clearance.

While it is hard to guess the reason for a relatively minor design decision like this, it seems that using four fins would complicate the tail design. Specifically, the airship would need to have a lower gondola or an X configuration for the tail, which may or may not impose a weight penalty on the tail structure.

As you note V control surfaces tend to be a net weight penalty once you factor in the higher loads placed on fewer surfaces. However, when the choice is between four small surfaces and three larger ones, the latter is likely to be more efficient.

You also note that the loss of one lateral surface would create a rolling moment, which is true, but this is the one situation where an actual "pendulum effect" (sigh) can be observed: the buoyant lift of the airship is directed against gravity, so it has a stable equilibrium point with the gondola pointed down, which simplifies the control problem.

Without knowing the critical load cases for that tail, it is hard to give a definitive answer, but this stands out as a plausible one.