I might have to do with the mechanic that breeding Nidoran female can result in not only eggs of itself, but Nidoran Male as well, and they were simply too lazy to code that same little complexity for Nidorina and Nidoqueen as well. It just was carried over in future gens because they were pretty stubborn about changing things about Pokemon until Gen VI, and it wasn't until Gen VIII they they changed up Egg Groups for pre-existing Pokemon, but even then it was merely adding a second group to Pokemon that previously only had one.
GF Staff 1: Okay, it took the whole roll of duct tape, but I managed to stick on the mechanic for Nidoran that it can have either male or female offspring.
GF Staff 2: What about Nidorina and Nidoqueen?
GF Staff 1: Well when you breed them the game will check if they're part of the female Nidoran family line thus the code will carry over.
GF Staff 2: That's... not how that works. We'd need to attach the special breeding code onto each of them as well.
GF Staff 1: Well, we're going to need more duct tape then.
GF Staff 2: I'll just put them in the Undiscovered Egg Group for now...
(Each time a new generation is released and they remembered about Nidoran)
GF Staff 1: OH, right, we need to attach the special breeding code onto Nidorina and Nidoqueen! Did you get the duct tape?
GF Staff 2: You know all these years it felt like I forgot to get something. I'll just write a memo to order some and keep them as they are now.
Joking aside, I can actually see them not wanting to mess with the code any more then they have to so just made Nidoran (F) the only one that can breed. Of course that was back in Gen II where looking at the game funny caused glitches, by now they should have structured things they could more easily make that a module and attach it onto the Pokemon which require it. (Note I said "should have").