They normally don't bother the polyps.
I've seen amphipods living in between the polyps with no harm at all.
I've had systems full of amphipods and zoas with no problems!!
They do eat algae from between the polyps. They help the zoas.
There are many, many species of amphipods and, generally speaking, we don't need to worry about the herbivores.
Now, if you have the bad guys, then they should be eliminated.
Many people hate all the amphipods because they don't know there are "good guys".
Bottom line is: if there is something eating the polyps you'll need to find out what that is. Sometimes you'll think it's the amphipods but there is a nocturnal snail, for example, and you try to kill the good amphipods instead.
Some people reported before that they had so many amphipods in their systems that the polyps were irritated, not damaged (eaten) by them. Well, that's bad!!! Even though they could be herbivores, if they are irritating the polyps because of their excessive numbers, that's another story...
If they are doing fine, then leave it alone doing it's own thing and enjoy. :thumbsup:
Hopefully others will post their experiences with their tanks.
Grandis.