If you're looking at a "normal" mono droid application (compiled with something like Xamarin) then you'll see some of these structures in the APK/ZIP'
File in the
assemblies directory will be the Mono/.Net code and can be reversed using those normal tools.
classes.dex is a normal Android Dalvik executable file (dex) which can be reversed using the usual tools (baksmali, IDA Pro, etc) - though it should just be the stub loaded to start the Mono engine.
The files includes in
lib/**/*.so are native shared libraries which are compiled into an ELF ARM file. These are normally going to the the monodroid engine (
libmonodroid.so) and potentially other plugins that have been used by the developer. These would require ELF ARM capable disassemblers like Hopper, IDA Pro, r2, etc.
In the specific example above, the only non-Xamarin code would be located in