I thought the problem was created by cleaning my iMac w CleanMyMac, however, I used CleanMyMac to solve the problem, at least so far. I set the app to use Privacy cleaning mode, as well as SmartScan. I don’t know why it worked, but iCloud was able to repopulate my password list in Safari after A Privacy scan and clean.
I encountered this problem and this is the only thread on the topic I could find so I thought I'd post my solution here.
The passwords list is linked to spotlight.
If you have changed spotlight settings and, as in my case, removed 'system preferences' from spotlight search, then it can't find them. I think it was that but in any case retick the boxes, close and reopen safari and they will reappear.
I will go through them later to be sure it was the system box, but I can't see what else it can be.