C'mon shl you can do better than that
Her father the reverend thinks Liz has some serious problems.
The cracks are problems, flaws in her character, weaknesses, that sort of thing.
Her cracks are so deep, her weaknesses and flaws go all the way to the center of her being. They aren't just skin deep, they are BIG!
So deep even the light of God (Gods power, love, forgiveness) can't even get to the bottom of her flaws.
It isn't a common idiom, it is just writing