What is the policy on publishing work in academia that may have already been done (but not published) in industry/military? I am interested in pursuing an area of computer security that is very likely already being studied by security professionals in industry and perhaps the military as well. Some of it is published, but I imagine some of it could also be unpublished work that companies and the military might not want to share with the public.
I could see my research group independently developing some unpublished techniques that probably are already in use in some form or another by existing companies who don't wish to share those to the public. In this case, is it acceptable for me to publish this as my own research, given that I have no affiliation to the company in question (assuming such a company does exist, which could very well be the case)? If I do publish, can I be in trouble for publishing work which these companies/military don't want the public to be aware of (but which I developed independently)?
It is fully acceptable to work on, and to publish, results on topics als researched in secret by companies or security agencies. From an academic point of view, there is nothing wrong with that, and neither from the point of view of stealing intellectual property. (But I'm not a lawyer!)  Whether those companies or agencies would be unhappy with you publishing some great new technique for breaking cryptosystems - probably not, but unless you believe in conspiracy theories, this is likely not be an issue.  (They might try to hire you, though.)
There have been precedents, e.g., on the best algorithms to factor numbers, or some cryptographic algorithms.  (I'd have to dig out references for that.)