about only time hand throttle ever used is for backhoe work. to many turns and and down slopes, getting around trees and like when mowing. to use hand throttle. even on my long straight away dirt road, i simply do not have long enough road to put hand throttle on.
for the old ford 555C TLB, i think manual states to lower RPM's between 1-4 gear shifting. the gear shifter, shuttle shift lever by steering wheel have clutch buttons on them. and the FEL stick also has a clutch button but is noted not to be used for shifting.
all in all, just thinking about how a hydraulic transmission works and gears in general... i would say let off the throttle. when shifting. or you are more likely to cause pressure relief valves to go off, and cause extra heat build up, and in that more wear and tear on the unit.
i generally let off foot throttle regardless when going from backwards to forwards or vice vs., so i do not rock and get the machine to start bouncing. (i like a smooth ride, nut a bunking bronco).
while a the hydraulic system might handle going quickly from forward to reverse and vice vs. (and i tend to use it heavily with loader work and turning around). i do slow things down. (not a young kid that is a ram rod, with foot on pedal and through the floor board)