For as phenomenal is the game is, we sure are getting some lame cop-outs in place of tying up loose ends.
Edit: looks like the spoiler tags render correctly on the web page, but not all apps support it.
tl;dr
It was magic and just disappeared and people are used to magic so… yeah shit’s gone, yo
…and it sounds way cooler IMHO. “Secret Stone” sounds like something a preteen would use in a short story about a superhero they just made up, or maybe a placeholder name that they never bothered to change.
I’m just going to pretend that they ARE called Sacred Stones and Hyruleans just pronounce it a bit differently.