Plutonium was first synthesized in a cyclotron by Lawrence's group at Berkeley. I don't know what energy they used so I don't know if they needed the extra coils, but they did know of the effect and must have considered it.
Also, U235 was separated at Oak Ridge using machines called Calutrons invented by Lawrence that might have encountered the same problem -- at least they must have considered it.
Klystrons were used in WW2, and the beam current of a klystron scales as the beam voltage to the 3/2 power (due to space charge limits). Modern klystrons operate with relativistic electron beams, but I don't know if any of the WW2 ones did.
At Los Alamos, various techniques using energetic photons and electrons were used to diagnose implosion systems in development of the plutonium bomb.