This. The fact that Ghost-Types can breed has no bearing on the fact that they are, indeed, ghosts or spirits of some kind. Yamask has already been brought up, it's literally said to be the ghost of a dead human in its Pokedex entries. While not all ghosts are specifically dead humans, all are spirits, demons, or ethereal beings of some kind.
They can breed and hatch from eggs for the same reason that inanimate objects like Magnemite, plants like Sunflora, and even mammals like Rattata can hatch from eggs. Gameplay convenience and consistency.
If you're bringing up the pokedex entries, then you have to think about who wrote them and how they got their information.
Well given that Pokedex entries are the only clue we have whatsoever into the nature of the Pokemon, they're kind of all one can talk about unless they want to talk about the anime, which has little resemblance to the games. If you disregard the Pokedex entries you might as well forget discussing the natures of Pokemon at all.