When you talk to the first Milfanito in the Shrine of Amana, she tells you that when they sing, the little ones dance, the little ones grant comfort to those who bear death and dark. She also tells you that she stopped singing because you approached her.
From what I've seen, none of the creatures in the shrine have brought me any comfort at all, so do we find out what the 'little ones' really are?
The 'little ones' are the fireflies that can be seen in this area. When the Milfanito sings, the fireflies will make the lizardmen (enemies in the water) passive, and they won't attack you unless you get really close to them.
When the Milfanito stops singing, the fireflies scatter, and the lizardmen become much more hostile.
Here's a video I just googled illustrating the principle. Watch the cloud of fireflies in the upper right:
