Your problem isn't due to obsfucation. It's because JVMPI never saw the romized classes being loaded since they are by definition already loaded before JVMPI started. Here's one thing you can try just for a profiling run:
1. Build CVM with CVM_CLASSLIB_JCOV=true
2. Run CVM with -Xbootclasspath/p=<your path>btclasses.zip
You should be able to find btclasses.zip in CVM's build directory. The CVM_CLASSLIB_JCOV option is a hack to get CVM to send simulated classload events for all romized classes (by loading them from btclasses.zip) to the JVMPI agent (in this case, hprof). CVM_CLASSLIB_JCOV (and CVM_JVMPI) is not an option that you will want to use in your deployed system because they have an impact on performance.
Note also that JVMPI on CVM will only allow you to gather profiling stats on interpreted runs. If you are running with the JIT, you should consider using the -Xjit:profile=<output file> profiling option instead.
Let me know if the CVM_CLASSLIB_JCOV hack does what you need.