The benefits of well-factored and modular code, in my understanding are re-usability and organization. Code written in a big chunk all in one file is difficult to read, and re-using small portions of the code requires careful copy-pasting, rather than include statements.
In particular, with regards to Javascript, I came across an example recently that got me thinking about this. A comment was made on SO to the effect that, if you are not including your javascripts conditionally on a page-by-page basis, this "represents a failure to modularize JS code properly". However, from a code re-use and organization point of view, there is no reason to consider what happens at page load time. The code will be just as readable if it is written in a bunch of separate files and then mashed together and minified before being served. The rails asset pipeline, for example, does just this.
When I first encountered the asset pipeline, my mind reeled and I started wondering "how do I make javascripts load only when needed?" I read a few SO questions and an article on the matter, and began to think that maybe I shouldn't worry about what happens to my code after it "compiles".
Is the purpose of writing modular code purely a human-level activity, should we stop worrying about modularity after the code starts running? In the case of Javascript, should we be concerned that our scripts are being mashed together before being included?