I am concerned with the inherently weak signals from satellites. They are at risk of being overwhelmed by more powerful transmitters that attackers may use on the ground/sea. Spoofing may be a problem, unless it is a subscription model where signed or encrypted communication is established.
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I absolutely agree with you. Anyway, as you spotted on your article, other navigation systems are available, and the key for autonomous navigation usually is a proper sensor fusion system integrating different sources, and also it would be necessary to have a failure detector for when the different systems are diverging. In my opinion, we won't see fully autonomous systems at sea, you spotted properly that a good captain is the best navigation system, maybe the crew will be reduced, but there will still be a maintenance team and so on (predictive maintenance and automation are progressing, I know but...).
The thing with subscription model GNSS is that deploying such a system, and then maintaining, is extremely expensive, with a very long term ROI. That is why this constellations are now deployed only by defense actors (European system -Galileo- is a European Comission "property" because ESA cannot have military intersts, GPS depends on the US army). But maybe, for some equatorial/medium latitudes what we will see will be regional GNSS augmentation systems (kind of a subscription based EGNOS/WAAS) that could help detect the spoofing. In fact... it is a very interesting idea to develop.