Gill length is determined largely by genetics. The growth potential depends on many other factors like nutrition, amount of dissolved oxygen, stage of growth, health status and other environmental conditions like water parameters and temperature. With two axies housed in the same optimal housing environment, provided with the same nutrition source, one could develop longer gills than the other, simply because their growth 'limit' is set by their genes.
The gill length itself is not a direct indication of gill health as i have often mentioned in other posts, however the gill cellular condition is an indication of gill health. Frequently, there is an area of overlap whereby poor gill health result in shortened gills. However short gills can be healthy too. The answer lies in looking at the microscopic architecture of the tissues. Two different axies, both with short gills, one healthy and one with pathology, if i were to sample gill biopsies from them, the healthy one will show gill tissues that retain their integrity and architecture with plump healthy cells, the one with pathology will show sick dying cells and the gill tissues becomes very friable.
With axies housed at warm temperatures, their gills become shortened but more importantly demonstrate signs of degeneration.
Cyanobacteria is indicated in a lot of pathology in both aquatic species and mammals. I am not surprised if they cause gill pathology. They cause opportunistic infections as well that can directly affect body condition and gill health.