Is there any certification for Aircraft Security that Software Engineers can accomplish?
I am unaware of any individual certifications for engineers related to avionics - security or general SW development. Caveat: This is based on my experience. That's 24 years of civil avionics development which followed a USAF career in R&amp;D, mostly space systems. I'm an aero engineer by schooling and my work is primarily defined as 'systems engineering' and management.  

Fundamentally avionics development is no different than any other product development. We define and develop hardware and software to perform specific functions on aircraft. The skills are essentially the same as the auto industry and even some consumer products. For the software side, this means real-time embedded applications -- not PC, web, or client/server apps.  

The biggest differences to other markets is the level of regulation and the life span of the products. Everything we build has to be certificated as part of an aircraft under a Type Certificate (TC) or Supplemental Type Certificate (STC) or as an 'appliance' under a Technical Standard Order (TSO). And even then the TSO'd product installation has to then be certificated under the aircraft's TC or STC. Because of the regulations, change is expensive so the products tend to have a very long life span. There are updates along the way, but you very seldom see wholesale product redesigns until the product is almost unsupportable or there are changes in the regulations.   

Certification is about demonstrating that the product complies with the rules. In the US, that's Title 14 Code of Federal Regulations. That means focusing the entire business to meet the rules. That includes internal development processes and procedures and a quality program that's compliant.  

Industry standards such as SAE, RTCA, (and EUROCAE in Europe) are the basis for most of these internal procedures. RTCA DO-178C doesn't tell you how to write code. It sets a standard for a SW development process that will produce the necessary artifacts for certification and theoretically result in SW that meets the necessary level of safety and design integrity. The company has an internally defined software development process that is compliant with DO-178.  

As for security, RTCA DO-326A, Airworthiness Security Process Specification provides guidance. It doesn't tell you how to build a secure system. It defines a process that will allow you to identify the security risks and ensure that you address the risks.  

So what's the best way to learn the avionics business? Seek employment with an avionics company. Avionics is a niche business. There's no big educational pipeline to feed the industry. If you have the fundamental engineering skills and a willingness to learn, you can get a job in avionics. That was the basic criteria I applied when I was a hiring manager at my last employer.  

As to the basic skills; For a SW engineer I would look for SW design and coding experience. Real-time embedded experience is a definite plus but not a deal breaker depending on the specific job. Most companies I'm familiar with use ADA, C, C++, etc. Getting familiar with the industry standards helps (and shows initiative) but it won't make you an expert.