“..If these guys hijacked their own airplane, isn’t it quite likely that there is detailed representation of their planned route and destination on Captain Shah’s machine?”
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I doubt it. At this point no one knows (we think) what the intentions of the perps that caused this were. So far, the distances of flight that are suspected are not long for this type of aircraft so it is impossible to even hypothesize about the flight mode (manual versus on board flight system) that was used and of course, where the plane went at the end of its flight. This could take a real long time to resolve.
If I were running the investigation, I'd want to grab an image of his hard drive, together with a forensic examination focusing especially on recently deleted simulator docs.
It appears whoever did this overlooked a little something:
https://twitter.com/rjonesy/status/444540040123658240
Transponder off. Check.
ACARS off. Check.
Satcom off. ... ping ... ping