This never used to be the case, but lately when I wake up my iMac, my HHKB is unresponsive until I unplug it and plug it back in. It definitely didn't do this before the past month or so, was always just connected all the time.
The way I'm waking up the computer is to click the mouse, which is wireless, and runs through a little wireless receiver which is plugged into one of the two USB ports on the back of the HHKB. So that tells me that at the very least, the receiver is still connecting to the mouse (and the computer) enough to make it work. But even so, the HHKB stays unresponsive to typing until I unplug that cable and replug it. I'm doing that from the keyboard end, btw, since it's easier to reach.
Also of note: occasionally, the mouse will suddenly stop working right in the middle of whatever I'm doing. The fix is to just unplug and replug that little wireless receiver, then all is well again.
I'm not connecting via a hub of any kind, just one of the iMac's built-in USB ports. I've tried restarting the computer.