Sorcerers are prisoners of the Divine Order, being transported to a secure location. It makes just as much sense for the prisoners to be armed as it would for prisoners in our world to be carrying AK-47's on the prisoner transport bus - none. There is no logical reason at all for the Magisters to allow prisoners to have weapons. No, not even "in case of monster attack".
If the prisoners are armed, they can rebel and get control of the ship, then they can take the ship elsewhere, to places other than the prison. That is not in the best interests of the Magisters.
It is common sense to not let prisoners have weapons. There is no sensible reason to allow prisoners to have weapons. Allowing prisoners to carry weapons on the ship is the OPPOSITE OF IMMERSIVE.
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At Fort Joy, that is the secure location from which prisoners cannot leave. It is valid to complain about guards allowing prisoners to carry weapons as breaking immersion there, but it is less of an obvious problem. But it's more forgiveable for gameplay reasons. There is no gameplay reason why you need a weapon before all hell breaks loose.
If you want reasons why the Magisters should fear prisoners, than just read this thread, two people have said that they killed all the Magisters as soon as they got up from their bed. I tried it myself and several magisters died in the ensuing fight. I could have done more with a better build.
