AH! Yes, that shrine. Again, forgive me, I haven't played Majora's Mask in awhile. From what I can remember about the shrine, it is a holding place for something. The 'braided' paper that hangs from the ceiling is dealt with Japanese seals. Did the shring hold Majora? Maybe, but I haven't been in the shrine in a long time to give a for sure answer.

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Atheism
The belief that there was nothing and nothing
happened to nothing and then nothing magically
exploded for no reason creating everything and then
a bunch of everything rearranged itself for no reason
whatsover into self-replicating bits which turned into dinosaurs.
Makes perfect sense!