I imagine, throughout Spirit's time away from the Cimarron Herd, The Eagle kept Esperanza up to date with how her son was doing. Of course, I've got no evidence to support that, or even to indicate that the horses could communicate with the Eagle. But, to me at least, Esperanza didn't seem overly worried about Spirit when we saw her in the movie. My theory is that she didn't worry about him because The Eagle brought her updates about him.
Lineart (c) WolfGirl50
Background (c) Spirit:SoTC