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I believe it does happen. Quite a bit maybe. I have seen a few cases, like your talking about, where the setup is right. The husbandry sounds on key. But, the chams are just reoccurringly ill. And the keeper tries everything to correct anything that may be wrong. Almost becoming obsessive about it all. Disturbing the cage, thus stressing the cham.
I think stress of any kind is BAD. But I think that there is a difference between constantly messing with your chameleons and keeping a close eye on them. Taking them out everyday or looking into the cage every five minutes IS too much stress, while watching them at a comfortable distance once a day looking for early stages of a problem is very important. As I am sure you know, most problems in chameleons are very successfully treated if diagnosed early enough.
Some chams there is no comfortable distance though, and any attempt to look at them is stressful. The ones that I have that are this way, I keep their cages far away from high traffic areas and thick with plants to make them feel more secure. I handfeed these regularly so I can get them to come out of the thick foliage, then I can give them the once over. This behavior type would definitely perish if you took them out everyday and handled them. Yet, I have others that try to reach for me anytime I come near their enclosures, ehibiting no stress signs whatsoever. However, I still keep handling and disturbing them to an absolute minimum. These are always the more vigorous eaters and breeders as well. They are also the ones I hold back for my breeding projects. My numbers of excessively shy individuals in my stock are gradually decreasing with each generation. Though its arguable if this is a correct selection criteria, as most arent this way in the wild. Shy behavior types probably survive quite well in the wild. Whereas, the bolder ones are more readily eaten by predators.
Its possible that genetic weaknesses caused by inbreeding, or starting with weak/sick breeding stock, or even breeding chams when they are too young could account for some of the chronically ill chams. Breeding under these conditions certainly compromises the overall health and vigor of the young being produced and may make them more prone to infections and such.
Some chams just seem to me to be weaker for no apparent reason. Maybe these should have been picked off early in the wild by natural predators. There are too many breeders that are almost too successful, it seems, at raising the weaker babies they produce nowadays to a healthy size. It used to be normal practice to cull the bottom 1/3 of the clutch. This is hardly heard of anymore. Maybe part of the problem is from nobody doing this anymore. Removing bad genes from the gene pool is necessary to benefit the species as a whole. I dont know if I could do it, but it makes sense.
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