Multiple examples of automated ships executing jumps in Traveller adventures here seems to have missed one: Annic Nova. And this was in GDW publications.
Correct GMing of robots should result in additional penalties for highly unusual circumstances. A sophont astrogator may alter the settings because, intuitively, the plotted result seems wrong. Without the ability to quantify the effect of a strange phenomenon, some approximation may be required and perhaps an intelligent astrogator is better able to fudge the amount than a computer program or robot that lacks as much creativity. Not saying the robot can't come up with something, but maybe the robot gets even more penalties than the human would have.
So you can buy an expert system that gives the ship Astrogator-3 in most circumstances and Astrogator-0 when the manure hits the rotary oscillating device.
I took this approach IMTU along with a general prejudice against automated control. And full robot control (not just supplementing human crew in every key position) would be considered illegal (voiding the insurance policy) for any merchant vessel taking on passengers or for a ship landing at major starports.
You end up with human crew because people have a prejudice against trusting their safety completely to a machine. You may get away with expert system gunners, or doubling up some positions (a highly rated expert pilot system, a highly rated expert astrogation system, and a human pilot/astrogator who monitors the systems and assumes control when necessary), or using robots to fill out secondary positions (chief engineer must be a person but if you have a couple of robots with expert systems on the relevant skills working all the time you don't need three engineers on the ship).
Also, robots are expensive. If it costs $360,000 each for those engineering robots that is more than the basic salary for an engineer. And the cost of the robot must be financed up front while the salary of that engineer can be paid out over time.
Also, a human engineer may receive medical treatment on a low tech world while that robot engineer cannot be repaired without access to appropriate parts. The higher tech the robot is the harder it can be to fix it. (same issue with designing a TL 15 merchant vessel instead of the basic tramp or far trader. You get better performance and/or more cargo space but the tramp trader can be fixed in many places where the TL 15 trader can't. (but your hull is made out of bonded superdense. We don't have the equipment to work that material....)
I like the way this works out. Traders avoid dependence on robots because you can hire a replacement engineer easier and cheaper than buying a replacement robot. But some villain with an entirely robot crew is still possible as an exception where having a crew that never gets drunk and talks too much is worth the cost.