They exist in FSA but tbh to me their culture felt entirely different. But then that’s not really anything unique to them in this series at this point. As far as their disappearance in TP goes, possible we just never really go to where they might be hiding out there, but I always had this feeling maybe Ganondorf turned them into the Bulblins if they might not have agreed to follow him in his conquest. Nothing to really substantiate that, though.
But yeah just to throw my two cents in here, think it’s definitely meant to be the same place. Have multiple ideas on what might have happened to it…perhaps Ganondorf, not having anyone to open up the Sacred Realm for him in this timeline, cursed the temple in a similar fashion to the Deku Tree, hence Armoghoma and all its children infesting leading to the temple falling in disrepair.
Other one is a bit simpler, larger leap in logic but not necessarily impossible is the shard of the mirror of Twilight itself was able to travel back through time either using its own power or that of the Temple itself. I guess my assumption was just that when Zant destroyed it, it just flew off wherever, but maybe he had more a hand in where each piece ended up. Hard to say whether many of the creatures are his minions or if many of these monsters just naturally end up following these pieces with a sense of desire not dissimilar to how it influences Yeta.