They are not totally necessary but if you have room, I would absolutely do it. They project the terminals from potential arcing like Diggs said, if you don't have anything covering them. They also give you a good, simple and clean way to mount the battery, yet easily remove it when needed.
I think the biggest reason to install your batteries in a battery box (besides a cleaner install) is in case the batteries spill or leak battery acid, it won't leak all over your boat.
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