LaTeX syntax within knitr::kable tables is not being processed using bookdown::pdf_book. It works fine with rmarkdown::pdf_book. A minimal reproducible example is here:
(Named test.txt to satisfy github attachment rules. Rename to test.Rmd)
The short answer is kable(..., format = 'pandoc'), but here is a longer story about the caveat: http://tex.stackexchange.com/q/276699/9128 kable() produces LaTeX tables by default for the LaTeX output of bookdown because of this issue.
kable(..., format = 'pandoc')