With the help of AppleCare support, after a very lengthy exchange spanning 6 months, this issue finally got resolved.
It turns out that photo and video original files were still erroneously being kept in the iCloud storage, even though I had deleted them completely from all GUI interfaces. I discovered this by downloading the entire library to my iMac using the Download and Store Originals settings in Apple Photos, and then in manually inspecting the
~/Pictures/Photos Library.photoslibrary file, by right-clicking the file in Finder and opening it with Show Package Contents.
I was then able to see old photos and videos that were supposed to be deleted long ago; which led me to understand that they were also "stuck" in the iCloud storage and therefore held my storage space "hostage" at a higher plateau than necessary. This had forced me to increase my storage plan.
The photos and videos not deleting properly happened pre-iOS 9.11, and it's not certain if the bug causing the actual issue is still alive in later iOS versions. However, if you have under unusual circumstances encountered this bug before the update to 9.11, the originals can still be stuck there, because iOS updates will not get them out of limbo. If looks like you have used up far more disk space/iCloud storage than the amount of photos and videos in your library can account for, I suggest that you inspect the
You will then need Apple Support help to reconstruct your iCloud photos library which their engineering support team can do, once you've explained the issue to a AppleCare senior adviser. Just be warned that they are not used to this issue and a lot of explaining may be needed to get them to take the case seriously. In my case, I had to collect a lot of evidence and do some real argumentation to get them to understand that there was a problem in their system.