Thanks.
All that's entered in the console consistently each night at midnight is:
Notification centre - turning off do not disturb, and re fetching information.
And bluetooth seems to restart itself as well.
Two drives are directly connected to usb 3. The others are by a new hub, also usb 3.
Nothing else happens at midnight, (not that I'll mention on here!)
Actually I have had a thought, with hindsight, I have always just presumed they unmounted, and remounted quickly. I have never witnessed that. Just presumed. They my never have unmounted in the first place, it might be a simple bug whereby the notifications pop up when the notification centre restarts. I will check tomorrow night and be watching.
I am fully aware I have probably answered my own question. Thank you for your help!!