The theme manager won't replace all theme-* packages, at least it's not the initial idea. It will provide a central mechanism to register themes and to choose and apply a theme at subsite and user level (and class/club level in .lrn).
As of packages that have "shared" icons, the idea is that common icons should be defined in a theme and not per package. That doesn't mean that package can't have their specific ones.
Theme manager project has just started so specifics are not defined yet and many questions have no answer yet.
