Node.js basically tried this — every package gets its own copy of every dependency in node_modules. Worked great until you had 400MB of duplicated lodash copies and the memes started.

pnpm fixed it exactly the way you describe though: content-addressable store with hardlinks. Every package version exists once on disk, projects just link to it. So the "dedup at filesystem level" approach does work, it just took the ecosystem a decade of pain to get there.