In
this article Hylian Dan has formed a theory considering blasphemy in Stone Tower Temple and Ikana. I would like to take this theory a step further by saying it's not just defying the goddesses what happens here but also the worshipping of a great opponent of them, the dark interlopers (later twili, or shadow tribe (japanese)) Besides that, it may well be possible that the realm that Majora had been sealed in by the goddesses is linked to or the same as the realm of the interlopers.
The first clue to this can be found in the
stone tower doors As you can see they depict two half suns, one red, one yellow. These can be viewed as a rising and setting sun. Dusk and dawn are the moments when there is twilight. So the doors seem to refer to the twilight.
Multiple references to the interlopers' power (in the form of the fused shadow) are also present.
This statue with a door in it, when turned upside down resembles Majora's Mask. But upright, it shows several similarities to
the completed fused shadow
Besides that, we see symbols resembling
Midna wearing the fused shadow. They can be found
on the boss door,
on the temple flipping gem The symbols refer to the immense power wielded by the interlopers and are featured on key points in the temple. So we could certainly speak of a certain form of respect, fear or worshipping.
Igos du Ikana says a lot about light and darkness and (before the fight) prefers the latter: "Oh, insolent one who has brought the abominable light into the dark land of Ikana…"
He later refers to the darkness as a curse, seeping from the temple: "In order to bring true light back to this land, you must seal the door to the Rock Building that is spewing out a dark wind." (quotes translated from the japanese version of the game (see theorizing resources))
The darkness consuming the world is also (in a different way) present in Twilight Princess, so we know that some gateway to the realm of the Twili can cause this to happen. perhaps that is what we see
here The giant mask, found in the temple has some things in common with
this one, belonging to Zant. If we go into extremes, we might even be able to compare the temple's entrance to Zant's head because of the light in the eyes, the finger on fire pointing to the sky can be seen as a tribute to Zant's magical abilities. (perhaps those of one of his forefathers)
These are all signs that the people of Ikana may well have encountered the dark interlopers at some point in time and that the realm where majora's mask was sealed is related to the one where the interlopers where put away.