I'm afraid that initially, you will have to go through your entire photo library and put your pictures in folders, assign tags etc.
There is no miracle app that does that for you.
Assuming you are an Apple user, why don't you use the Apple photos app?
It does not keep copies in albums and 'all photos'. When you 'put' them into folders or albums, they get the folder or album assigned as an attribute, and will not be duplicated and moved there.
In case of 'real' duplicates, you can easily find them, combine them into one, or delete a copy.
The AI of the app does a decent job of pre-identifying items and scenes. Eg I can search for 'snow' and it will show me many (all?) pictures with snow. Or, when searching for 'bathtub', it shows me baby fotos of my kids sitting in a bathtub, and I had already forgotten that I had this picture! And I never created a tag 'snow' or 'bathtub'.
If you start assigning names to faces, it will begin to scan your library and try to identifiy these faces in other pictures. This also works decently. Even with images from people in different ages (not 100% accurate, but good enough for a start).
Of course it won't (and can't) catch everything, and personal items, events, locations etc. you will have to add manually.
But there is a keyword manager that even allows you to assign a shortcut to your most commonly used keywords, so you can bulk-add keywords/tags to a multitude of pictures, simply by a keystroke.
I had about 20k old pictures, scans from negatives or slides, no tags, people, dates, locations or events assigned, and it was a multi-year project for me to get all these attributes and tags assigned properly. But now that I have it, the combination of my tags and the AI identification of things is amazing, and blazing fast.
The app is not flawless, nor are other apps.
I tried Adobe Elements and ACDsee, and will stick with the Apple app, 1st its free, 2ndly it does a decent job, and 3rdly it's well integrated in the Apple ecosystem.