>>44992349Pokémon shit, canonically noted in the Pokédex. If they have one hole, they have to and if they're intended to be expies of real world animals into a fantastical, albeit biologically correct setting, we can take it as read they have behaviours equating real world animals, therefore do actually have genitalia and bump uglies to increase the population. The fact the daycare attendants also are incredibly vague, while at the same time explicitly clear on how an egg appears (they don't know how it got there, but do know none appear with two boys, two girls or two unknown gendered pokémon (unless one's a ditto and even then they really aren't sure how) indicates it's sexual reproduction (egg moves and inheritance of mixed stats from the parents is another).
But yeah, write your headcanon if it helps you cope with the graphic truth.