What I’ve wondered, since gen 2, when genders were introduced. If you can have a male and female Pikachu then can’t there also be the option to have a male and female Nidorino or nidoqueen? Why is this the only Pokémon to have separate genders each get their own Pokédex number?
Well, from a game programming standpoint, Nidoran (m) and Nidoran (f) only have separate dex numbers because in Gen 1 they were the only sexually dimorphic pokémon. To deal with this, rather than just calling them "Nidoran" and having formes (which GF hadn't even done yet), they made the two Nidoran have separate entries. Once Gen 2 hit, and the pokémon's sex was now something potentially all (or most) pokémon could have, the Nidos had already kind of been screwed up. You couldn't turn Nidoran into a single entry without removing one Dex entry turning the Kanto dex from 151 to 150 and renumbering everything starting with them across all pokémon media. I assume that headache was more of an issue than it was worth at the time, especially since Gen 2 was originally going to be the last generation.
However, going from Gen 2 forward some pokémon that are recognized as alternate sexes of the same pokémon species have been given their own entries, but rather than having the simplistic naming convention that the Nidos have (just slapping a male or female symbol in the name) they actually have different names. For example, it's generally accepted that Tauros and Miltank are the male and female of their species. Same goes with Volbeat and Illumise. Honestly, if way back in Gen 1 the Nidos had been dealt with the same way and named Nidoran and Nidoron or something this wouldn't even be an issue now. The only issue is they have the essentially the same name.
As for why you can't have a male Nidoqueen, the answer is simple. The Nidos have a branching evo line based on their sex. It's the same reason you can't have a female Gallade or a male Froslass. If the Nidos had been introduced in Gen 3 the dex would have likely only had one entry for "Nidoran" and the male and female forms would just be gender differences similar to how Hippopotas and Hippowdon have different colors based on their sex. Then to get Nidorino/Nidoking and Nidorina/Nidoqueen you would need to catch/evolve the Nidoran of the respective sex, which is the way Espurr/Meowstic work as well as Kirlia/Gallade and Snorunt/Froslass.