Personally, I don't have any rules-mechanical reason why a sophont intelligence (as opposed to an electronic intelligence) is required to use the Astrogation skill. On the other hand, every polity in my game requires sophont oversight for starship operation to be legal and license-able - getting caught running without suitable oversight could mean hefty fines, impoundment/confiscation of the ship, possibly criminal endangerment charges - having someone with a valid (or at least passable) Astrogation certification/license is pretty much an economic necessity, but there's no reason why a group couldn't use a robotic astrogator in practice. Just make sure the paper/electronic trail is taken care of, in case that next naval/customs inspection team is run by a particularly hard-case martinet...
I like the idea of high-automation ships, though, and I'm toying with the idea of a new campaign setting. Current idea is a drastically misjumped colonization effort from the Long Night era which wound up a long way rimward from the Solomani Confederation. I'm thinking about waiting for the new World Builder's Handbook, but I'm also sketching down several ideas. Probably looking at a two-to-three sector space several sectors outside of Charted Space, so that recontact is going to involve a mission somewhat on par with Deepnight Revelation. The misjump occurred far enough in the pass that the stranded colony has now become the core of its own pocket empire, and there are probably going to be a few other races with their own empires. More or less, the idea is to use the rules of Traveller, but to take the various empires of Charted Space off the table. (Yes, humanity is genetically Solomani, but that's mainly an academic concept, of no real importance to the average person.) But anyway, the anti-robotics trope which runs through almost all of Charted Space is one of the things I'll be filtering out.
(Edited to correct a horrid directional confusion.)