My biggest criticism of this work is that it does not consider C++. Most of the big HPC projects today are written in C++, not C, and to the best of my knowledge this transition happened in the 90s.
My experience is limited to one single field, but all weather prediction models and climate models that I know of, are in Fortran. And I would count them as big HPC projects.
Trilinos is another C++ example, while PETSc and HYPRE are written in C.
My tentative conclusion from this is that newer projects tend to use C++ and slightly older projects use C.
Yes, there are things like ODEPACK, QUADPACK, and FFTPACK, but those are not under development anymore (as far as I know). The only widely used Fortran library still under development I can think of is LAPACK.
I did not count the occasional 'bespoke' code. There are still some Fortran applications in development for particular purposes (like MOM), but those are harder to survey.
Most users are usually fine with whatever the GUI allows and a bit of Python, but for those of us developing new models, Fortran is probably the most useful language, followed by C++.
A quantum Monte Carlo code will of course include a model, but I think people don't want to call it "software" because it's so research-grade and janky. "Program" seems better, but I think that implies that it's a static thing (not in a constant state of development).
The plural "codes" is used because usually a research team has historically implemented a bunch of models into disparate codebases.