Chloramine is basically a combination of Chlorine and Ammonia. The addition of the Ammonia provides stability and longer disinfection potential to the Chlorine. It does eventually disassociate in water into Chlorine and Ammonia. While any Chlorine neutralizer will negate the effects of the Chlorine, the Ammonia remains. While normally not at a level high enough to cause any real damage, the additional Ammonia is added to the pond water.and in a pond that already may have some issues with balance in the Nitrogen cycle, this could cause a problem, especially when large water changes are being performed.
Vanish does not neutralize Chloramine, only Chlorine as per the manufacturer.