It is hard to say what may have caused this, as we cannot see your device and do not know how you have been using your iPhone. A system update does not delete photos from iCloud.
Where are you looking for your photos? In the All Photos album? In the Days? The Recents album may be sorted differently from before after an update. Look in All Photos for your photos. And check the Filter (in the menu with the three dots (...) in the upper right corner. A filter could be hiding some of your photos.
Photos will only be removed from iCloud Photos, if you delete them from any of your devices that are syncing with iCloud Photos as well (or someone else, who is sharing your AppleID). If you are running out of Cloud Storage, iCloud Photos may delete some of your older photos after some time.
Turning on iCloud Photos will however delete photos, that have been synced to the device from a computer, as synced photos are not compatible with iCloud Photos. when you backup your iPhone to iCloud, the iCloud backup of the iPhone does not include the photos, if iCloud Photos is enabled. Do you have a backup of your iPhone on a computer, that you made, before you started using iCloud Photos? A backup on a computer will be saved, until you delete it, while the iCloud backups are rolling backups, that may be automatically deleted after some time.
After a system update it may take a while, until photos have been restored from iCloud to your Photos Library.