I'd like a citation on that. Obviously, Classic Traveller didn't have Virtual Crew as a thing in the main rules, so by default nothing could be automated. But there's nothing in Book 2, Book 5, or Book 8 that says that that I am aware of. But it does say that you don't need a navigator unless your ship is greater than 200 tons and you don't need an engineer unless your ship is greater than 100 tons. I no longer have my copy of the Starship Operator's Manual or other Megatraveller rules (grr...), so can't say if it got introduced then.
Classic Traveller misjumps weren't a function of a skill test. They were a random event that could happen because of bad maintenance, using unrefined fuel, or (in the 1980 version) not having enough engineers for the size of your ship.
In CT, the computer did the work. The Navigator doesn't make a skill check for plotting a jump course. That's what the Generate program and Jump programs were for. As far as I can tell, the human control was just part of the Third Imperium's 'no free willed machines' issues. The Annic Nova was able to jump on its own just fine.
Here's the Generate Program from Classic Traveller: "Generate creates a flight plan which will govern the use of the jump program. The navigator or pilot can input specific co-ordinates into the computer concerning a destination, and the generate program will create a flight plan to take the ship there. In cases where a generate program is not available, starports have single-use flight plans (in self-erasing cassettes) available for all worlds within jump range for Cr10,OOO per jump number. The generate program may be used independently and produces the required flight plan, which is then used by the computer when jump is performed."
Also, just as a bit of trivia: The pilot makes more than the astrogator and always has.