I did it. I know the Secret of the Magic Crystals.
And if you want to know it too, you can just play the game for 26 hours yourself.
Nah, just kidding. It turns out that when all five crystals are brought together, they will open a gate to another world. Once there, you reunite with your grandfather (I didn't realize he was missing), and together you "justify" his theory. I must confess, I'm a bit confused by that ending. Surely the existence of all these unicorns and demon steeds and whatnot are sufficient proof of the existence of magic. Or maybe people in this world believe in magic, but not in your grandfather's specific brand of magic.
I suppose it doesn't really matter, because that's the first time it was mentioned since the opening animation, and the game does not apparently change at all after you get the crystals.
In retrospect, I don't really regret the extra six hours I spent grinding out those last horses, but I am a bit embarrassed about them. I've walked away from better games than this, and I can't really explain why this one got under my skin. I guess it must have something to recommend it, if I could play it for so long. Yet I am definitely looking forward to my next game.