Interesting point you have in here...
First off: Jabu Jabu is just the king of the Zoras (which is strange and doesn't make any sense, as the king is supposed to be that fat Zora with a crown who's daughter is Ruto, who is clearly a princess).
Maybe some kind of evolution: Zoras started as ginat fish who, in order to survive (maybe because there were little fishes to feed a lot of those big fishes), and thus only a few of them survive, being them Jabu Jabu's ancestors.
Then Jabu Jabu laid some eggs (supposing Jabu Jabu is female), and, from there on, the species started to evolute, to the point some species finally laid eggs from which some Zoras came out.
That theory is highly unprobable, and it is more reasonable to think that Zoras are different species from the ones of Jabu Jabu, thus answering your problem.
Good question, though
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