Dual systems theory: in what sense are the systems 'unreal'?
What Kahneman means is that these are nothing but comparisons, or metaphors, to indirectly explain cognitive processing. Neither you nor I have physically seen these two systems exist, BUT the existence of such systems may be implicated through neural representations. Kahneman has used economic metaphors (concept of resources and their allocation) in his capacity model of attention (1973). (1)

The following excerpt from John B. Best's Cognitive Psychology, fifth edition (2) , might help. Here, he talks about the rationale behind using a metaphor (the information-processing or computer metaphor) in cognitive psychology:


  Because the information-processing viewpoint is necessarily abstract, why use it to study cognitive processes, especially when it might be possible to study the underlying neural processes directly? In other words, the students seem to suggest that we simply cut to the chase and study neural processes themselves. What stops us? Information-processing theories might argue that an abstract analysis is necessary because of discoverability problems at the neural level. It's true that specific relationships may always be discoverable between specific neural activities or locations, and particular cognitive or mental events... Despite this reservation, however, cognitive psychologists working in the information-processing tradition maintain that there are no guarantees that a general, discoverable neural representation inevitably underlies all specific cognitive events."


TL;DR: It's a metaphor, an indirect comparison to how cognitive processes occur, for ease of understanding.



1) There has been considerable debate regarding whether the concept of using strict, dichotomous systems is a good way to represent cognitive processing and why and how dual-process theories like Kahneman's fail in some aspects. Highly recommend reading some of the highlighted points in The Mythical Number Two by Melnikoff and Bargh (2018), published in Trends in Cognitive Sciences.

2) An edition of the book is available to borrow on archive.org and you may find this quoted text in the first introductory chapter.