Repair Library not working in Photo

If you have a Time Machine backup check the date when the issue started, duplicate your current library and replace it with the older one.

I suppose you have the option to “copy items to the Photo library” enabled in Photos app, if it's the case, create a new library and extract the originals from Library.photoslibrary/Masters and re add them. A quick Find inside the “Master” (.jpg, m4v..etc) folder will save you time to look in every subfolders

An apple article is there : iPhoto 6 and later: Rebuilding the iPhoto library - Apple Support

I see many of my original fotos in ... Pictures/Photos Library.photoslibrary/Masters/2016/ ... which are not in Photos.

Is that the Photos Library that Photos is using when you launch it? Check the name of the library that Photos opened in the Photos > Preferences > General:

The path to the currently open library will be shown at the top of the window.

If Photos is using a different library try to open your library in the Pictures folder by double clicking it. Repairing the library will repair the library that has been used last. You may have repaired a different library.

.. which are not in Photos.

Have you checked the "Recently Deleted" album and the "Hidden Photos" album?

Search for the filename of one of the missing photos in Photos. If the Photos are in the Masters folder for 2016 they have been imported in 2016, but the capture date may be from a different year, and they may be in a moment for a different year and be showing among the photos for 1970 or so.