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2. Is there a way to obfuscate hibernate mapping documents as well?
Not as far as I know. Unless your obfuscator is clever enough to rename fully qualified resource names in non-class files (and your class name references are fully qualified!). I don't know if any obfuscators can do this.
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1. How do I handle the situation when my java files will be obfuscated and the mapping documents still contain the un-obfuscated names? I can't use obfuscated names in the hibernate xdoclet as I can't predict them...
Don't rename the classes that have references in resource files. Renaming class files is just one part of the obfuscation process - you can still obfuscate these classes using other means e.g. flow obfuscation. Of course this depends on which obfuscator you are using.
Justin