It's something I first saw only yesterday and it didn't feel so annoying back then. Now it's starting to irritate me a lot.
Watching the koyukkuris die like that gave me an idea. I'd go and replace the koyukkuris with some random other (preferably shitheaded) koyukkuris. They'll say the Reimu and Marisa aren't their parents. I'd love to see how the parents would react and what unfurls after that.
Babies Yukkuris tend to be quite weak, usually when the babies are born, some preparations are made, either lower the forehead to reduce the height or prepare a lot of comfy and soft stuff to reduce the impact. Besides, since in the ideal scenario the parents are awake and aware of their birth, they would probably heal them or make them feel better if an accident happened during the birth.