I have noticed large amount of very large amphipods in my tanks as well, but after doing some homework and searching through Bob fenners FAQ's on WWM, i found that these crustaceans are supposedly harmless to corals and very beneficial to the system as a hole. But i am very skeptical of these statements because about a month ago i bought a small colony of yellow polyps. One night i was checkin out the tank with a flash light, and the yellow polyps covered with swarming amphipods. over the next couple of days the polyps would not open, and, eventually, the polyps disappeared all together. I don't want to jump to conclusions, but it does seem that these creatures devoured the polyps. But all i'm saying is, be aware that we all could be over exaggerating and this loss of polyp could something completely different.
also, i have a sixline and coral beauty, both of which each amphipods, and my tank is still swarming with them.