Resonance
I'm not sure I see how resonance could be set up (or sustained) in this system.
First, the fuel was cold and viscous to some degree. The non return valve is one way, thus tending to cancel any resonance (which is oscillatory in nature). Resonance requires a sustained oscillation with feedback loop, and in a system that normally would not excite resonance, if one were to form under certain specific conditions, it should be easy to break up the resonance with some applied external force. Just to remind you, there were operating boost pumps and operating HP pumps here, with one at one end of the fuel "column" and one at the other end. I would think the forces of the pumps should tend to break up any resonances that might form.
I think this applies so long as a major structure(s) does not provide the feedback mechanism, which would be harder to overcome by external forces. If major structure(s) contributed to the feedback loop, then the system would display natural resonance quite readily.
I also seem to recall discussion that the non return valve is in the suction feed flow path and not in the boost pump flow path.
Water hammer (or fuel hammer) is just a pressure spike created when a valve opens or closes (due to column momentum) and is not really relavent here I would think. Water hammer (or fuel hammer) does not normally restrict flow, but is rather a design consideration pertaining to maximum pressures seen by the system.
I stand to be corrected of course.