@mitu Well, as always thanks for the help. I don't think it's underpowered given my new 3.5a CanaKit PSU made specifically for the Pi4 and it's a powered USB hub. But I can't rule out an unseated cable or something because now it's back to working correctly. I'm going to keep the USB HDD connected directly to the Pi, since if that isn't seen on boot, then it won't have access to the romsets which explains why they wouldn't show up, and if the USB cable to the hub got jostled then that would also explain why the gamepad wasn't detected.
#OccamsRazor