I read the presentation and I think this is a serious problem.
What the security researcher is talking about is using unsecured communication channels (ADS, ACARS) to identify then attack an aircraft, compromising the FMS and possibly other systems.
From what he was saying it appears that there are ''zero-day exploits'' available for some FMCs, through normal data channels. Once in there, the attacker could do pretty much anything.
We tend to think of aircraft nav/data systems as being made up of isolated units but if there are communications between them, then they are vulnerable. You can do a fair bit with most FMCs: tune navaids, select navigation sources and even use them as backup dials and switches for when these fail. On the 777 you can be ''pushed'' route updates by ATC (or whoever is pretending to be ATC...) Once compromised, you could display to the pilot(s) ''situation normal'' but in fact be taking the aircraft off-route...