In most cases it’s not. It’s a game design decision to restrict exploration and gameplay scenarios that can break the experience the designers want to convey.
That’s about swimming on the surface, swimming underwater adds another more set of problems like navigation controls, the need to have an underwater terrain and creatures (more content needs to be created but games are expensive to produce. Also increases the size of the game files), it can be boring and therefore unnecessary if the design team does not dedicate enough time to make it interesting and fun, may not be consistent with the rest of the game concept, can break other aspects of the game and more.
Sometimes limiting the player is a smart decision.
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