The storm was the only cause, so it is in fact “of”.
It's not the direct nor the first cause.
Saying the satellites were lost because of the geomagnetic storm could imply that the satellites suffered some sort of electronic damage. Which, as I understand, is not what happened. That is why the nuance here is important.
In your case, there is no other reason for the boat to be lost but because of the wind and waves.
The nuance isn't that important. The implication that a geomagnetic storm can only cause magnetic/electric damage is just wrong. It's like implying a hurricane can only cause damage through wind and rain.
Starlink lost 40 satellites following geomagnetic storm