I did find myself wanting to introduce custom logic - like custom helper funcs for the Go templates - but there is no way to do this short of modifying and rebuilding hugo.
Specifically I wanted to use some functions from here: https://github.com/dustin/go-humanize
In the short run, it was fine. Since most of the data is structured I could write a script to modify the input data to prepare for output without modification.
Not sure about hugo's longterm plan for this type of thing, but overall it is an awesome project and would highly recommend over every other static site generator.