In xcrun simctl documentation there is an entry:
xcrun simctl shutdown booted - Shutdown a device
Bun when I call it from command line, the simulator is not actually shut down but is freezed instead.
How this could be solved?
The only workaround I found is to kill the simulator by its Process ID.
killall "Simluator"
Simulator.app predates CoreSimulator and still assumes that it owns the entire boot lifecycle. You should only use 'simctl shutdown' for devices that you booted via 'simctl boot'.