Why does it mention the three?
Malbim (Derech ha'Muskal): He shows the philosophers their mistake. There is a nature of begetting among animals - via mating, they beget like their forms. This preserves species in the entire creation. Sechel does not understand how this arises via mating. No impression should be left at all (refer to 30:19:1:1)! Hashem established the creation like this; it is not part of the nature of the Hiyuli (formless matter) and blending of the elements. Hashem commanded so, to make species continue.
Malbim (Derech ha'Pashut): After Agur's answer (not to inform about the planned rebellion), it brings Meshalim and metaphors about Alkum, the slave who rebelled and seized kingship.
What are "Nifle'u Mimeni"?
Rashi: They were covered from when they passed from my eyes, and I do not know to where they went. They rush to be hidden from the eye.
Malbim (Derech ha'Pashut): They do not lave any mark where they went; it is as if they did not go there at all.