I'm not sure that in 1986, the state of the art used 400 Hz as a frequency for timing the signals and the circuits.
The 400 Hz is not related to any kind of timing. It's about getting size and losses of transformers down. With increasing frequency, the efficiency of transformation increases, thus producing less waste heat. At the same time sizes of the transformers shrink for a given load, thus saving in cost and, equally important, size.
It's the same principle that gave us the switching power supply and its high efficiency and low losses. Here also the primary AC gets turned into a high frequency one so a rather tiny transformer can be used instead of the huge copper piles in a linear PS. Unlike the Cray, a modern power supply uses several kHz instead of 400 Hz.
I'm also not sure that if 400 Hz is needed, that motors are the best way to generate that.
It's not so much about exact 400 Hz, as the conversion of a lot of power. In the mid-1980s power semiconductors weren't at a point where such loads could be handled fully electronically (*1). Coupling a motor running at mains frequency and a generator on its output shaft that emits a higher frequency current - basically the same as the motor, just more poles. Prior to power electronics this was the only way to transform frequency. For example, rail power in Germany (and others) is 16.6 Hz while mains is 50 Hz. Beside rail power stations with generators producing 16.6 Hz, there where also converters from main power using motor generator units.
Beside the advantage in lower copper cost, more compact design and higher efficiency, such a motor-generator inherently works as a UPS. Due to inertia, short interruptions on the input side are smoothed out, making the operation way more reliable. In fact, depending on the size of the motor-generator, it could even supply the whole machine (including disks) for several seconds. That's more than enough time to write a savepoint (*2) and have an orderly (emergency) shutdown. That's why mainframes often have a special power fail interrupt state.
I'd guess it's too imprecise for timing a supercomputer.
As said before, it's not about anything in timing, but size and efficiency of the power conversion.
400 Hz in particular was chosen, as this was already standard since the 1940s for certain military equipment and airplanes. It's always better to use some standard and standardized equipment that comes with it. So Cray didn't have to create their own converters.
*1 - and even today, as we can do it, we still use the same trick. Just now it first gets rectified, then turned into high frequency pulsed (several dozen kHz) current, which still gets transformed to whatever is needed and rectified again.
*2 - A savepoint is a recording of the actual state of a job under program control that allows restart when restored. It's not the same as freezing the program, more like an automated save to files when closed.