I'm not sure why you think socket-based communication would have security concerns (use SSL). It is often a very good approach as it is language agnostic, assuming that you have a well-defined communication protocol. Have a look at Google's protocol buffers, for example - they generate the required Java classes and streams.
In my experience, file systems (especially network file systems) are not well suited to such communication as they are not necessarily tuned for messaging (I've seen caching issues result in files being not picked up by the target process for example).
Another option is a messaging layer (AMQ or Tibco for example) although this will likely involve a greater administrative overhead (plus expertise) to set up.
Personally I would opt for a pure-socket approach because of its flexibility and simplicity. You will be in complete control.