JD-EE you are correct that the FFT window needs to be about 100Hz for the 10ms pulses. A bit frequency shift you get anyway by doppler effect, since the towed array needs to move. However you should gain a lot of signal to noise if you know that there is a 10ms pulse train to look for you can coherent digitaly decode. It is more than only the S/N gain with the 100Hz filter which is comparable to a Morse code filter. You know what morse code to look for and this gives you the additional S/N like in GPS. So the time stability of the ping interval is equally important. I think that the ping frequency should be best compatible with the sensitivity of typical towed arrays from hunting subs. They have all the DSP power on board you need for this job. Make the pinger compatible with its capabilities.