[TP] Why are the fused shadows in the temples to start with?

I was wondering about the plot of TP. I'm not sure if it's ever discussed why the fused shadows are there in the first place.

Using the forest temple as an example I have two theories: 1.) They were sealed there to prevent anyone from using their power. I like this theory because it gives a reason to the existence of the temple, but that doesn't explain the goron mine. The seal could be weakening over time, or it could be weakened because Zant tried to obtain the fused shadows when he cast Twilight over the area. But Rusl said the forest was getting dangerous even before the twilight overcame it. This could just be a precursor to Zants invasion though

2.) Zant had them and was attempting to hide them so nobody could use them against him. This theory doesn't have the problems of the last one but I don't like it as much. Mainly because it becomes "why wouldn't he use them?" But I feel he can't, because he didn't use them in his final fight against link when he had 3 of them.