Yeah that can happen, though in my experience it's far more common that IDEs are broken by some janky custom build system set up by people that use Vim or Notepad++.
I think you're also right that some languages make this harder for IDEs than others. C++ is probably a worst case. Something like Java is trivial because the file structure matches the namespaces. It's probably not a coincidence that every Java IDE I've used has absolutely top class code intelligence tools.
Yeah I went from Java to JS and was surprised how much worse the code browsing experience is.
C is probably not as good as Java but I remember using Eclipse the first time with C for operating systems class, and being amazed with what a large codebase looks like and how easy it was to maneuver.
Intellij's webstorm does js pretty well - almost as well as their java offerings.
Having said that, VSCode these days are also pretty damn good.
Yeah Typescript in VSCode is pretty good. I guess because the VSCode developers use it all the time!
C++ contributes a lot tot his problem. IIRC you can't even reason about C++ code until you've parsed all of it. Undoubtedly, IDEs employ clever tricks and shortcuts, but even they can do only so much.
(Or maybe it's just a problem specific to C++ projects and IDEs. The largest codebases I worked with, the ones where I hit this problem, were C++ ones.)