Disclaimer: I am the author of Hakyll.
What Hakyll gives you is an EDSL on top of pandoc, which allows you to more easily specify how different files should be processed. It is much like a specialized make
on top of Pandoc. It also offers some other features which are useful for building static websites, i.e., manipulating URLS and HTML.
I think the main difference between yst and Hakyll is that Hakyll is on one side more customizable (since the configuration is just Haskell), but probably harder to get up and running as well.