I can see where that's coming from, but this is a one-sided view. It misses the obvious conclusion: interface agents (to use the article's terminology) are
complementary to direct manipulation interfaces, not a replacement.
Direct manipulation is great at discoverability, when I'm exploring the choices available to me, but it sucks if I'm looking for something specific (for software with a minimum level of complexity, like Photoshop or Excel). Interface agents have the opposite characteristics, as the article explains. So, they're complementary techniques.
To provide a simpler example, not involving AI: if the user is a domain expert (say, a graphic designer), the ability to search for and perform a specific action quickly is far more important than discoverability. For example, the user may already know that GIMP provides a feature for drawing a path but have only used Photoshop in the past and now they just can't find that action.
Aside: it is telling that established design software like Photoshop / GIMP has such a bewildering maze of menus even today. But if you take Google Chrome, for instance, it provides a stellar searchable user interface [1].
[1]: http://vickychijwani.me/searchable-user-interfaces-are-the-f...