According to my understanding, nWave doesn't have a command line interface. It fact, it seems to be unnecessary. After all, debugging is an interactive process. Unless you already have a list of signals in your mind, which you would like to pre-load into nWave. If it's so, then you can modify signal.rc file and load it into nWave when you open the program.
Second, if you want to view signals across several scope of the chip, you can do it easily with verdi. Let say you want to know why the valid signal is asserted at 1026.5 ns, you simply double-click on the rising-edge of iot_out. Verdi will automatically lead you to the corresponding source code (across multiple hierarchies):
If you further double-click on cnt_gray, verdi will further lead you to the driver of the signal:
If you want to view the waveform of gray_cnt, left-click on the signal to highlight it, hit Ctrl-W to add it to the nWave window:
Is this what you want? I think these features are already useful enough?