Even if this was possible, wouldn't CPDLC be a more serious threat? I'd imagine it's relatively easy to hack into one of the international systems and pass along incorrect info. All you need to do is tell the pilot to do the wrong thing and they will do it. If the FMS does the wrong thing any pilot worth his salt will question it.
One of the aircraft I operate uses a "windows" based FMS with integrated ADSB, SBAS, XM weather (obviously useless in Aus) and satellite 3G connection; Several integral links to ground based communication, but I fail to see how anyone could "hack" any of these systems and access the FMS. Not to mention without me noticing.