If we're talking about Aegis, they replaced UYKs with PCs and the realtime constraints are very soft (hundredths of milliseconds); that's hardly embedded, unless you mean embedded in a ship. And yeah, Java works there way better than the CMS-2 they force fed engineers with before.
In any case, those systems are far from having the physical and technical constraints of the actual system on a missile, plane or satellite; simply put, a 50ms delay to know the speed of a remote object is acceptable, a 50ms delay to know the speed within said object isn't.
To this day, and to the best of my knowledge, 95% of hard realtime logic is C, C++ and Ada or a combination of them, when not custom ASICs and FPGAs for low latency and high throughput tasks.
If we're talking about other systems, I'd like to know about them.