I know this question was asked seven years ago, but I thought it was a really interesting one.
You might assume (as I did) that it had something to do with female Pokémon only being able to lay eggs of their own species, and Nidoran's status of practically being two different Pokémon that share a slot would confuse the game. You'd be wrong.
Apparently, Nidoqueen's inability to lay eggs dates back to before breeding was a game mechanic, going all the way back to the Pocket Monsters Encyclopedia (1996), four years before the release of Gold and Silver. It states that, "[Nidorina] is the evolved form of Nidoran♀, but upon becoming Nidorina, has lost the ability to lay Eggs." No further explanation or reasoning is given.
By this logic, the entire existence of the Nidoran line is dependent on Dittos being in the area, or female Nidorans just deciding not to evolve. And they just made that a thing one day, for fun, not even knowing that they would cause me a mild headache almost three decades later. If you were looking for a rational answer, then I am truly sorry to tell you that rationality left the door twenty-six years ago.
It just does not make sense. Why did you do that? Nidoran can still breed, and they made it specifically able to give birth to both genders of Nidoran. Was it really necessary to stick to the canon established in the random book that nobody read? You couldn't even put it in the dex entry? Some uncredited author can just, delcare Nidoqueen's infertility in passing, and everyone will just agree??
In short, the answer to your question is known only to the Japanese guy(s) who wrote the Pocket Monsters Encyclopedia, and you will never find them because they went uncredited. The author is listed as "Creatures, Inc." (the company that does modelling and some spinoffs I think), and they have over 200 employees, so it could really be anyone.
TL;DR: Game Freak is a lawless hellscape, logic is a mere suggestion, and the Nidoran legacy is doomed to fall.
