Eggs with shells are only laid outside of water. This is because shells are meant to limit water loss. Amphibian and fish eggs are laid directly in water, so I'm assuming shells are bad simply because they're not needed? They may prevent certain nutrients from crossing through the outer membrane of the eggs. Also, perhaps amphibian and fish eggs "breathe" through some sort of process on the membrane, which means this process would be blocked if there was a shell.
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