Most of the FADEC systems have dual alternators, dual controllers and dual sensors, but people still don't run them very often. Probably the most popular one I know of is in the Rotorway Exec series helis.
SDS also sells a (non-redundant) EFI system that's used in a couple of aviation applications. My dad is using a SDS system in his Jenny.
You also can't run a modern closed loop EFI system because of 100LL (avgas). The lead in it will destroy an oxygen sensor. So you're still stuck with a mixture lever in most cases.
And that's just the experimental crowd. The cost of certifying an EFI engine into an existing airframe would make a retrofit cost prohibitive. Most people won't spend an additional $20k at overhaul time to add fuel injection and digital ignition. It would take a bunch of hours at +20% efficiency to make that back.
A couple years ago I heard about a company selling a modern ignition system packaged into a mag. The idea was to replace one mag with the digital ignition and leave one mag as a safe backup. I don't know what happened to them. Last I heard they were selling units and working on certification for the Lycoming O-320/O-360 and Continental O-300 engines.
Also, I just looked up the guy in the article. He sells his digital ignition systems for around $2k. He's managed to get a STC for a heli, so that's some progress in the right direction.