I think that, no book entirely dedicated to the work with the netCDF data has been published yet. However, after some googling, I discovered that the following book:
Elsner, J.B., Jagger, T.H., 2013. Hurricane Climatology: A Modern Statistical Guide Using R. Oxford University Press, New York.
contains at least three pages (156-158) with some information how to work with the netCDF files in R. You can read these pages on Google Books (e.g. at books.google.com). Since this book was issued in 2013, the readers are referred to the 'ncdf' package which is no longer developed now. Nevertheless, the same author published a successor of this package entitled 'ncdf4'. I recommend you to get familiar with it through its help or its reference manual (e.g. at https://www.cran.r-project.org/web/packages/ncdf4/index.html) because the functions therein have different names from those incorporated in the older 'ncdf' package.
Also, I discovered an excellent website on this topic: