I've seen plenty of ground station and mission control software in Java. Actually in space a bit less likely though... A lot of that is running in RTOS environments that Java isn't well suited for (forget garbage collection, some flight software projects go as far as to ban dynamic memory allocation)
"Aegis Battleship Weapons System"
http://www.artist-embedded.org/docs/Events/2011/JTRES/Slides...
"French radar system for ballistic missile tracking and measurement"
https://www.militaryaerospace.com/defense-executive/article/...
"NASA Ground Control Station for Multiple UAVs Flight Simulation"
https://www.semanticscholar.org/paper/Ground-Control-Station...