I have not had issues with my ehd and I have been thinking I was just really lucky. However I think your explanation is spot on. I have a Seagate (pre WD buyout) and I hooked it up to my computer first and turned off the power management so it would stay on all the time. Then plugged into Hopper. I have not any problems from day one on original Hopper when it was first released. I am into the Hopper 3 and still working.The problem with it not connecting is a power setting in the firmware itself. The Hopper powers down the USB port when inactive for x minutes to save power. It’s a feature used in windows by default. I always see people asking why their EHD isn’t working without re-plugging it in everytime they want to use it. With windows the setting can be changed. Unfortunately with the Hopper the end user can’t do anything about it.
If it is possible you could transfer content to Hopper, hook up ehd to computer (you will have to format drive) then turn off power management (assuming your ehd has it, might want to check with manufacturer first). Then hook back to Hopper and let it format to Hopper, then transfer back to ehd. Long drawn out proceeds, but might be worth trying.