Is there (some form of) penetration testing in aviation?
There is lots of testing in aviation, in every step of the process from paper designs to an actual airframe. For situation based training the aviation industry turns to the tried and true method of  

Simulation

This is similar to software in many regards (and often uses computer based simulations). Simulator tech has come a long way in the past 35 years and full motion simulators are a great way to get very very close to the real thing. If you want to test out a situation where you knock out some random approach lights, throw in low visibility and some wind shear there is no reason to risk an actual aircraft, and a pilots life. Just queue it up in the sim and see how they do.   

When it comes to the physical testing of say an airframe the FAA (and other bodies) also tend to take the "...before we let it out there approach" to testing and certification. In other words before an airframe is certified for production it will undergo extensive flight testing that physically pushes the airframe and exposes it to situations it should never encounter in normal flight. Omega Tau does a great episode with an Airbus test pilot that goes deep into whats involved in this, its worth a listen. 

The biggest difference in aviation is that you have control over the end to end situation. In computer security you simply cant tell people "please be careful, if you use this encryption it may break in the following cases and we dont know how to fix it". On the contrary in aviation you have the ability to train pilots and more importantly you have the ability to make (or enforce) a no-go call. If we know an approach system only works down to certain minimums you simply don't fly if the weather is below them, unlike in computer security where the system is expected to always work and always be secure and in a lot of instances, always be up.