because the hylians were a race of white skinned people that lived in the magically mild climate a days travel away from the hot desert sun. thats why their skin is white. later, when everyone moved to the hiltops of the world while everything was flooded, there were more tanned folks too btw.
why exactly there were no variantly skinned gerudo is a mystery, seeing as how they abducted men from outside their female only tribe to procreate. but! they literally might not be naturally dark skinned, but also simply tanned.
probably, there simply are races in that world and their genetics dont work the same way human genetics work. who knows exactly.
that thing with the islamic symbol, first of all, you realize who created that game? the japanese. at a time when we barely had any problems with muslims or islam. their game designer didnt think anything of it, same way they didnt think any of adding quran verses in the fire temple song or using other symbols from islamic religion or mythology. they did it because they needed symbols for decoration.
of course, the gerudo were somewhat representing arabs. they had a tribe of desert dwelling people and they chose to take from the real world desert dwelling people. in part, they were inspired by arabic folklore to some extend. they're a mixture of amazons and alibaba's 40 thiefs. did they dig into the stereotype bag somewhat? sure. did they mean anything by it? no. does it make the game racist or discriminative? no. its called context, use context to make sense of the world. as much as you would love to believe that context is irrelevant, it has never been in the history of mankind. and it never will be. and the people that act as if it was, will always end up being the laughing stock of history.
the only thing that gets discriminated against in the zelda games, is evil and darkness. twilight princess somewhat makes a point of it, they even sealed the gateway between the normal and a dark world (right after throwing the biggest evil they knew of into that world too)
the sheika (not exactly a race, but more of a clan, like basically the hyrule version of ninjas) weren't decimated in a genocide. they were servants of the royal family i think and at some point, during some kind of war, they were mostly wiped out by whatever enemy that attacked them. its never clearly revealed, but considering these lands are full of monsters and dark legendary creatures from all kinds of dimensions, and zelda has always been at the center of all these creatures attention, these things happen. they're not the only race to have disappeared from hyrule over the many many decades that the complete storyline goes through
while the gerudo always lived in the desert, were a society of warriors and thiefs and its probably for either of those reasons, together with the stealing of men, that they werent the most welcomed people in the world outside of their selfproclaimed kingdom.
in addition, dark witches governed their tribe and supported the spawn of the devil too.
also, you seem to be trying to make the point that since there was war, there had to have been discrimination. when war can be about so many things. land, power, ressources, ideals, sure.
and maybe, one or two wars were literally started because there were people praying to something else than the goddesses that created the world (mostly dark wizards and evil spirits)
but then, you cant really call that discriminatory. because they know gods and evil god equivalents exist. and they know that only three of the known gods actually dont want to drag the world down into chaos... so you cant really compare that to real world religious discrimination and war.