The elephants are known to take warm waters of the lake up in their nose, it is possible that like humans it sometime goes up higher to cause PAM? Aggression followed by deaths have been reported in zoos, could it be due to PAM?
I don't know about Elephants but there are some exotic animal papers such as the case in a tapir that I linked the citation to below. It seems certainly a possibility. I would expect however that zoos do some sort of autopsy when an elephant dies as they are fairly expensive and high visibility animals.
Lozano-Alarcon F, Bradley GA, Houser BS, Visvesvara GS: 1997, Primary amebic meningoencephalitis due to Naegleria fowleri in a South American tapir. Vet Pathol 34:239–244.
We know surprisingly little about animal infection with many opportunistic organisms, whether protists, fungi, bacteria, or other microbes. Many of these opportunistic pathogens are probably more common in humans than we realize, but things like Naegleria, Balamuthia, and Acanthamoeba have been noticed more in countries with robust surveillance and clinical disease reporting requirements, even though they doubtless occur in other areas, perhaps even to a greater degree. In terms of animals, there is little doubt that opportunistic amoebae do infect them, as the tapir study cited above and other reports suggest. Opportunistic microbes such as Legionella are also known to infect animals, but this is poorly reported and poorly read even when published. So, your idea is a good one, but there are many things that could cause some of the conditions in elephants that you describe, so any particular etiologic agent should not be assumed. Some serological evidence might be sought for an easy look, but the actual organism must be located and identified in diseased tissue before we can make any legitimate statement. Good luck with your search!
A mandril died in the San Diego Zoo of encephalitis due to a free-living amoeba, later called Balamuthia mandrillaris. An brain autopsy was performed and this amoeba was found. I think the same should be done to elephants with suspicion of death by free-living amoebae.
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