How can I put this without offending? A time scale of millions of years is almost meaningless to cichlid immunity in the present for several reasons.
One is how the immune system of bony fish works. It has two components: an innate (inherited) and adaptive (acquired) component. There are volumes upon volumes of science papers on this as it continues to be studied at the cellular and biochemical level. Inherited immunity means earlier generations pass on the ability to quickly recognize and fight pathogens that have been encountered before. Adaptive immunity is a system that recognizes
newly encountered foreign invaders and then prepares a defense to fight them. Without citing some heavy, boring science paper, the simple proof of how well this works is the problem of invasive fish species, including cichlids, in various places. If cichlids, plecos, asian carp, snakeheads, pacu, etc. are happily living in foreign waters in the US, presumably encountering new pathogens or water mineral profiles, they probably can (and obviously do) handle unfamiliar pathogens in our tanks-- some of the issues have more to do with conditioning and acclimation, stresses we put them under, drug resistant superbugs, etc.
Cichlids did not invent their dual immune system. Cichlids fossils go back something like 46 million years, bony fish 400 million years.
Additional reasons millions of years ago has limited impact (especially in terms of limitations to immunity) on the present is that pathogens themselves are constantly adapting and most animals, including bony fish, adapt as well. It's not just that, but habitats change over centuries or thousands of years, sometimes decades. Cycles of climate, limnology, and geology dramatically change the landscape. Lakes and rivers come and go, change course, or see changes in chemistry. The watershed that is now the Amazon River flowed in the opposite direction before @ 10 million years ago, but other changes are much more recent. Pleistocene (ending @ 11,700 years ago) climate, flora, terrestrial fauna, and rivers themselves were different from the present and the current (Holocene) period has also been a period of change:
Geomorphology and evolution of the late Pleistocene to Holocene fluvial system in the south-eastern Llanos de Moxos, Bolivian Amazon
Seven paleochannel generations are identified. Significant changes in sinuosity, channel widths and river pattern are observed for the successive paleochannel generations. Our results clearly reflect at least three different geomorphic and hydrological periods in the evolution of the fluvial system since the late Pleistocene. Changes in discharge and sediment load may be controlled by combinations of two interrelated mechanisms: (i) spatial changes and re-organizations of the drainage network in the upper catchment, and/or (ii) climate changeswith their associated local to catchment-scale modifications in vegetation cover, and changes in discharge, inundation frequencies and magnitudes...
The particular stretch of a particular river that species "X" now inhabits and is adapted to may not have existed not so long ago, or if the location is the same, conditions may be different. Therefore, this 'species' is either much the same, and consequently adaptable to the former conditions, or it has changed in some way to accommodate the changed habitat. This would be a big subject all its own, but science now understands genetics to function more like software, with if/then logic acting on various triggers and environmental inputs, compared to the "blueprint" genetics of our former school days. This changes the model many have for how all of this works-- I'd go into it further, but this post is already long.
So, adaptation-- whether to microbes, habitat, climate, or water conditions-- is dynamic and ongoing. Individual species come and go as conditions change or as they colonize or retreat from various locations. Some will be more specialized to certain conditions than others, but because cichlids have existed for millions of years doesn't lock them into a written in stone state etched by millions of years. Among the adapting systems are immunity, feeding, and range of water tolerance, even while basic morphologies of some clades (geophagines and haplochromines, for example) have remained much the same for tens of millions of years.
Don't get me wrong, I'm not saying this means you can throw Lake Natron cichlids in a tank with discus, or you shouldn't quarantine, or that you can feed your Neetroplus an all guppy diet, or that temperatures too low or pH too low or too high can't depress immune function, but some go to the opposite extreme and either aren't aware of the natural range of certain groups (like discus), insist their comfort zone is more limited than it really is, or extrapolate the wrong conditions to the wrong species or population of a fish.