Thanks Henry and Ernest.
From your comments, I understood that
1. Generally instrumentation happens on copy of original source.
2. they use counters to get the info if its traversed
From online resources, I found they would use CGLIB to do bytecode instrumentation. Normally, after a testsuite ran we can see the code coverage. So this means, the testsuite ran against instrumented classes and not the actual one.
I know that there are some security issues and some stuff related to digital signature. Dont they play any role.