no, the pods wouldn't be eating the zoas.
Either you've got a predator in there that you just haven't been able to detect, or it's something else in the water parameters.
I have several batches of the same zoa colony in my tank. In three of the areas, they're doing beautiful, but in one of them (which
BTW also has worse lighting), they often stay shriveled up and don't look so healthy. It's strange, but the edges of the individual polyps are rough and chewed up looking.
I also had/(maybe still have?) the tiny little snails that Renee hinted at (sundial/box snail); however, they never seemed to bother the zoas too much...they just kind of hung out in between the polyps munching at the rocks...
I hope you can figure out what the problem is. Try putting the rock in a different area to see if it's the lighting.