Hello.

I have 2 small ponds one with only Fathead minnows and the other Fathead and Crayfish.

The one without Crayfish is full of minnows, but the one with Crayfish the Fathead decrease every year.

Is it possible for Crayfish to eat Fathead eggs under the rocks.
A+

Yes

I doubt it's a major factor, but I've watched some types of crayfish catch small minnows also.

In some of our rivers here, using minnows for bait, you'll catch more crayfish than fish.

I don't know of anything that a crayfish won't eat, in general. Some plant types are probably avoided, but if it is animal based...they will eat it.