"It's a fantasy world" does not mean people in the world should act illogically. They should do things which make sense according to the rules of the world. Letting prisoners keep weapons is not a thing which makes sense according to the rules of the DOS 2 world.
The Magisters are rounding up all Sourcerors and taking them to Fort Joy, whether or not they want to go. It is not an optional thing they can turn down. They are taking them by force to the island, and the goal is to not let them escape. Once they are collared and on the island, it's less of an issue.
Letting the prisoners keep weapons does not help the Magisters with their goal of getting all the unwilling Sourcerors to the island. It puts the goal at risk by making it easier for the prisoners to revolt and possibly overpower the guards, then seize control of the ship and take it away from the island to elsewhere. Magisters would consider that a Very Bad Outcome.
Because letting the prisoners keep their weapons is Not Helpful and can lead to a Very Bad Outcome, by the logic of in-game characters, it makes no sense.
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As for Wendigo's power... if you look at the characters, she is level 5, all the Magisters are level 1. In terms of gameplay, it's not terribly unreasonable for a level 5 character to overpower a large number of level 1 characters. When you meet her later, you are probably level 4 or 5, and she is level 5.
