If you choose Java for your project it usually means you don't care a lot about latency and performance (you care some, but not all that much compared to, for example, linux kernel development). You care more about managing larger codebase, having easy access to whole lot of frameworks and libraries, good development tools and easy development / deployment process.
Developers who have experience with Java are inevitably people who have mostly had experience with those kinds of projects of which I would say most are corporate backend systems or Android applications. It really is difficult to find any other projects.
On the other C is inflicted pain of having much harder development environment for the size of the project. You only use low level language like C when you have a specific need. Maybe you need to develop Set Top Box software, or video codec, or some device controller, or high performance quant library, that kind of stuff.
So it isn't really fault of Java developers to not know the stuff. It is natural result of Java being suited to a different type of projects than C is.
Out of curiosity, what was the rationale for writing the system in Java? Were the tradeoffs not obvious until too late, was the choice of language dictated by higher-ups, etc.?