Dune is not a dependency manager, it is a build tool. Opam is the dependency manager. By default, Dune doesn't fetch dependencies, opam does that. That said, Dune does use opam, yeah.

And the next milestone of Dune is to become an alternative package manager via Dune package Management, using a store in a "nixish" way.

I suppose it is still going to use opam internally, right?

No, it is doing its own package management implementation.

So dune is going to replace opam? Where can I read more about this if so?

Package description, but it use its own engine.