And which implementation that you seem to imply exists DOESN'T suffer from this seemingly fundamental issue? You built this strawman, now defend it or stop waving your hands.
Of course not, all the code and data that go into the processor needs to go through the processor cache first.
My OP comment has an example of a JVM that doesn't read jar files as you mentioned, while executing native code stored in a JIT cache present in the hard disk, between invocations.
Google is your friend if you look for the respective documentation. Or, who knows, you could even download it and play around with it.
I'm out, please turn the lights off on the way out.