Does anyone know of any documented examples of airline accidents caused by hacked or otherwise deliberately compromised avionics?
Searching the NTSB Accident Database which also covers some international commercial flights for the key words "hack", "hacked" do not provide any results related to hacked avionics. Likewise using the keyword "tampered" does not provide any results related to deliberate tampering with avionics (mostly "tampered" wreckage).
There is one individual, Chris Roberts, who claims to have hacked into the In-Flight Entertainment System (IFE) to cause the aircraft to deviate from its course, however I find it highly suspicious. From a security perspective, I can't of any good reason to have the IFE network on the same network as any avionics, however that isn't to say that there isn't some possible connection. The FBI certainly didn't think it was very funny.
So as of today there have not been any aviation accidents that are attributed to hacked or deliberately tampered-with avionics as a cause of said accident. The closest thing I think you will find is pilots loading incorrect flight plans, outdated (or even pre-dated) navigation data, and other cases of pilots not correctly using the equipment.
I did read your original question and would like to clarify. Conspiracy theories, guesses, and internet speculation are not a replacement for hard evidence. In the case of MH-17 the wreckage was recovered and no evidence has been presented in the favor of hacking, while there is a lot of evidence of the shoot-down. Airliners even at cruising altitude can be shot down by surface to air missiles rather easily.
As for MH-370, until the wreckage is found we may never know (and even if it is we may never know). Black boxes do not have an indefinite life span especially if they are under water. Until then theories of that flight being hacked are just as credible as those saying aliens abducted the entire flight and they are living on Neptune in specially constructed Igloos.
No. Near as I know, current navigation and flight control avionics are separate from internet connected components, so 'hacking' them is physically impossible.
Now, more types of cockpit avionics are becoming Bluetooth compatible, allowing for interconnectivity with internet connected mobile devices or apps eg Garmin Pilot, ForeFlight, etc., allowing a person to download a flight plan into a GNSS head for example. Maybe some hacker at some point will analyze a security flaw within these avionics and be able to exploit this.
In addition, these systems often take software updates in the form of SD cards, USB thumb drives, etc. so there is a possibility of introducing malware into the system that way as well.
But even if a GPS head were attacked that way, there would be no means for it to gain access to the control systems of the a/c, the system could be manually shut down, and backup means of navigation used.
But in the era of Stuxnet and budding developments of cyber weaponry paralleling the development of the Internet of things, anything may be possible in the future; just not now.