Actually it does.
You just need to look to the correct JVM. Apparently people keep forgetting Java is like C and C++. There are plenty options to choose from and OpenJDK only plays the role of reference implementation.
If I am not mistaken IBM J9 is one of those JVMs.
Java JIT doesn't write machine code to disk. OS/400 does, and then it re-uses the machine code until it no longer exists (you move to new hardware) or the bytecode is newer (you change the program and recompile), at which point it compiles the bytecode to machine code and stores it to disk again.