No need for further consideration! Mother Reimu threw out the dead yukkuris in the nest. She tidied things up by rearranging the old newspapers and wood planks, and so Little Marisa and Little Reimu went to sleep in the nest, feeling safe and secure.
You should know by now that most yukkuri don't read too deeply into things. In their mind, the only moment that exists is right now, and the only thing they have to worry about is food and easiness.
Note that doesn't apply to all -- but she's a mother, and her most-important duty is to her children.
No need for further consideration! Mother Reimu threw out the dead yukkuris in the nest. She tidied things up by rearranging the old newspapers and wood planks, and so Little Marisa and Little Reimu went to sleep in the nest, feeling safe and secure.