As @splix said, deploying two app with different languages into the same appid seems to be impossible. So how about a workaround instead? Set a /pythonapp servlet on your Java app that will redirect all requests to mypythonapp.appspot.com via URLFetch.
The drawback of this workaround that come into my mind is that you are losing the information about the logged in user provided by the User API, so you would need to attach the information on the redirected request. Depending on the scenario of your app, I don't know whether this would be a show stopper or not.
EDIT: What I had in mind is what Peter suggested, using different versions rather than deploying them as totally different app, sorry that I mixed them up. Deployment to a different app would mean your Python app and Java app could not use a shared datastore.
The difference on my answer is that you could use URLFetches to forward the requests between different versions of your app. But having the redirection performed on the client's side as per Peter's suggestion rather than having it done on the server side as in my answer would probably be less hacky.