i don't know about the cloudy eye issue, because i've never seen it before in salt fish. i thought this was a very rare thing. apparently though, it seems to be common, as i've read multiple threads on this forum about people's fish having it. maybe i just didn't keep the fish long enough to see any issues.
meanwhile, yes- stress can and does lower the immune system and leaves fish susceptible to any number of diseases.
if in fact you have ammonia present, this is easily enough to stress a fish to the point of illness, if not kill the fish from poisoning.
water changes which are the same temperature and ph of the water you are taking out can never hurt a tank, no matter how often. i would do water changes until the ammonia was not detectable. mix large amounts of water with a heater, powerhead and/or an airstone overnight to completely mix it and level out the ph.