ProGuard only works with Java. It does not support any other language.
http://proguard.sourceforge.net/
http://developer.android.com/tools/help/proguard.html
The Corona Simulator and Corona Enterprise *always* compiles your Lua scripts into byte code. All of the compiled Lua byte code files (*.lu files) are then bundled into a single “resource.car” file, which is kind of like a tar ball (*.tar file)… and that is what’s put into the APK.
Regarding Corona Enterprise builds, if you build a “debug” version via ant/AndroidSDK/Eclipse, then the debug symbols are preserved in the compiled Lua scripts. If you build a “release” version, then the debug symbols are stripped out and your Lua stack traces won’t be of much help anymore.