this is absolutely disgusting
Conditions in southern lockups up until the latter half of the 20th century were harsh because life was hard in general and for a lockup to be seen as punishment, the belief was that conditions inside needed to be harsher than in general society. So yes, some of the boys likely died at the hands of guards and as is the case in lockups, some would have been killed by other boys.
The number of reported/speculated graves seems unremarkable for such an institution in operation for over a century. In the first half of the 20th century, nutrition was poor and so was healthcare. We forget what a toll diseases such as TB, smallpox, polio, measles, influenza, malaria, etc used to take on populations.
Florida was a wild, sparsely populated place in the first half of the 20th century. Life in general was difficult and communications were poor. For many of these boys, their families had already given up on them, or never cared about them in the first place.
In 1920, you couldn't just keep a body on ice while trying to notify next of kin. If next of kin were notified, you couldn't just load a body into a refrigerated truck and deliver it to a funeral home in South Florida. People back then generally buried their dead where they died and moved on.