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I always thought it was weird that Tetra and her crew are the only pirates in the vicinity of Windfall Island. When Tetra first brings Link to the Forsaken Fortress to track down Aryll, she says that it "used to be the hideout of a no-good group of pirates we used to compete with," which presumably means there are other groups of pirates. I suppose the canonical explanation for the absence of any such pirates in the game is that, now that the ocean above the former site of Hyrule Castle has become infested with Ganondorf's minions, only Tetra's crew is brave enough to travel through the area.
Ironically, this means that the Bokoblins are keeping the Great Sea safe from pirates. If people like Beedle and the Salvage Corp divers feel comfortable sailing around without fear of being attacked, and if the merchant Zunari has suddenly come to Windfall Island under the (correct) assumption that the area is conducive to profitable trade, then maybe it isn't so bad to have Ganondorf's forces on patrol.
Ironically, this means that the Bokoblins are keeping the Great Sea safe from pirates. If people like Beedle and the Salvage Corp divers feel comfortable sailing around without fear of being attacked, and if the merchant Zunari has suddenly come to Windfall Island under the (correct) assumption that the area is conducive to profitable trade, then maybe it isn't so bad to have Ganondorf's forces on patrol.