Speculating based on both writing large systems from scratch, and joining a group where a large confusing system was being used...
Diagrams are sometimes unnecessary overhead early in a project. Sometimes I’ve used them and seen other people use them for initial design planning, especially if management needs to be involved or approve the plans & schedule. But by a year later, the design has grown and changed, and everyone on board is so familiar with the code, but also so pressed for time and feature delivery, that making diagrams doesn’t make sense: nobody involved at this point needs them. Two years later, when the code is getting complicated and slowing down, and you’re onboarding some new people, that’s when it might help to sketch the flow of code.
FWIW, sometimes a good profiling tool will show you and let you explore call stacks, call graphs, execution charts, etc. I often reach for a profiler when I’m new to a codebase. Flame charts are a fave of mine. You can find flame charts in Chrome’s debug tools, or in compiled language profilers like vtune or valgrind. Here’s a decent article on how to use them https://www.brendangregg.com/FlameGraphs/cpuflamegraphs.html
Another issue is that well designed code bases diagram themselves by their module structure, while diagrams for poorly designed code bases may not help understand them at all. When code has too many side effects, or things are poorly or misleadingly named, when class boundaries aren’t well defined or the code has a lot of spaghetti, diagrams might not really help.
IMO two things worth doing are: get a mentor in any new codebase any time you can, and 2) start building your own arsenal of code diagramming tools, rather than wondering why or waiting for others to do it. Demonstrate the value of diagramming code to people around you and see if you can get it to catch on.