Actually Wheunis, a guy posted a howto on the official blizzard forums after he got it working on a emulator on his winblows pc. So that throws your theory out the windows.
Also, its java, and java is the easiest language in the world to decompile. Now I am sure blizzard took it a few steps futhers and made a lot of strings in hex ect to make it harder to figure out the code, but I am sure anyone can figure it with enough time.
The big thing here is, if the hackers don't have the serial you attached to your account, they can;t hack it, but I am sure if they can find that serial they can make minimal changes to the decompiled code and add the serial and tada they have a copy of your authenticator.
Which is why I wouldn't trust it on windows, but it can work on windows.
That being the case, if it has been done, i apologize.
Having looked over the case you presented from the forums, this was no everyday task though.
It might sound simple on first glance...
That being said, if i owe anyone for tattoo removal lemme know.
About the decoding Java.
Blizzard has taken very strong steps towards keeping that from happening. I'm not saying just because I cant do it, nobody can. I just don't have the time or resources available to run a decryption algorithm for the next 3 years to break their code lol.
Rest assured though, Tinuva is absolutely correct. Even if they do "crack" the code, they cant do anything without your specific serial number, and further they would also need your "synchronization code" (the code generated by the authenticator server that is saved on your device at the time of installation).
This code also changes each time you "resync" the authenticator application.
EDIT: Upon looking further into the matter, it would seem i was only HALF wrong. Yes the authenticator app will RUN on the emulator, but it seems that it loses it's original "security token" upon restart/close/exit/etc.
What this means is, each time you wanna use it, you MIGHT need to unbind your authenticator from your account, and rebind it. This will include a phone-call to blizzard to prove ownership before they will unbind the authenticator.
EDIT-EDIT: Further research indicates that the EU Guild, Nihilum, has managed to re-engineer the authenticator app into a usable, emulated, mini-java-applet for Windows XP/VISTA/7.
For further information see
http://www.nihilum.eu/news/
Dont ask me! I just found it!