I don't think that there's anything wrong with it, and I certainly agree that you should use what works best for you. Shoot, if it's good enough for LinkedIn, it's good enough for something. I'll leave the debate about apps that are ideal and not for node to others. That said, you won't catch me using JS server-side (or python client-side).
I think the analogy with an EDA like Eagle vs. KiCAD is not a great one, however. When you are done using your circuit editor, you get a set of files that are exactly the same regardless of where they came from, and the end product is a PCB which can't tell you which editor designed it. So the productivity thing is just your personal preference.
When designing an ecosystem for development, you're creating something for others to use. I think it's hard to ignore that the vast majority of the libraries for the Pi (and linux embedded systems in general) are written in Python these days. On top of that you'll find much more familiarity (and support) within the community for the standard LAMP stack. As I've said before, pushing boundaries of existing technology is where innovation is born. For me, it's just recognizing a time and place to do so.
C