I agree! I’ve wanted to add this feature for a while, but customer support and other bugfixes/more pressing features (like browse-by-filesystem) kept pushing this down the list.
My current thinking is that there should definitely be “exclude from library” (Xcode’s “just the reference”), and this is actually already implemented for images subsequently found in NoMedia directories.
Marking assets as “hidden” would require a new “only show hidden” assets view, which I’m currently thinking will just be a tagged search result (/search?q=hidden:true), as would “excluded” assets.
You can do this by clicking the paths in the asset info panel, which will replace the currently-displayed variant with the file you just clicked on.
Here’s a reddit discussion about deleting photos from a while back: https://old.reddit.com/r/PhotoStructure/comments/jaiz06/suggestion_delete_files/