Based on all the blogs and HN comments and comments here, that couldn't be further from the truth. Are these just things you learn from experience / mentors?
There's an analogy I've heard, and I can't remember where. It might be a Feynman quote I'm recalling...
It'd be crazy to start design work on an airplane, if you're hungry and want to go to the corner store a block away for chips. It'd also be crazy to try to walk to China, since it's a long way, and also you might drown. The approach you take to solving the problem of getting from here to there depends completely on where here and there are, and what else you want to carry with you.
I don't use namespaces and build modules for an Arduino project, or a simple command line tool. But for large projects, I literally can't live without namespacing and modularization.
The core task of programming constitutes very different activities at different scales, as different as comparing walking to building jet engines.
As far as where to learn these things: there are some books that talk about more broad topics than just how to use a particular tool/language. Those are more supplemental to experience/mentors, though.