I'm gonna take a crack at this, and for all I know it'll be spewing hot air, but what the heck.
Using OOT, WW, TP and MM as a general reference, the dungeons/temples are located within the strongholds of major races. The leaders of these races specifically tell you that they have been entrusted by. . .whoever, to guard this or that in the temple or in space before they make whatever it is magically appear. Now, in FSA, the items in question ARE in the temples, and they are specifically what the people are guarding, either from people or for one person in particular, the Hero of Time/Winds, etc.
So lets take the leap that the temples are taken over for any other reason than to dislodge the Powers of Light in residence, which is a VERY LARGE leap. Does that even make sense? Not really. Ganon doesn't tear apart the temples making sure that there's nothing useful in them! He wants to negate the threat of the sages, not to keep little Link from getting the Hero's bow. It's just that after Ganon swaths the places in darkness, badies move in, including the bosses. Now, SOME of these bosses have possible backstories and places within the timeline, but most don't, at least not extensively. So, being the biggest and baddest badie around, they would take up the big room. What skultula, deku, stalfos or fire slug has any interest in locked doors or chests? None. So the items that were already there remain there.
Considering the items we find are useful not only in the temple in question, but in the surrounding area, I would venture to say that the treasures we find are simply a reflection of the awesomeness of the race controlling the area. After all, if the Gorons are all like, "Yeaaaah we like da hammah!" then why wouldn't they put it in their sacred temple?
Just sayin'.