Please note: most of my answer is based on supposition and experience as a Director.
There are no references as far as I can tell (under cursory research) about superstitions related to the facade of a witch cracking under duress or to any similar behavior in the "Dark Shadows" original series.
It is assumable that the Director (Burton) does this for cinematic and symbolic reasons.
A witch (often like a vampire) has a lot of mythological license (along the lines of poetic license). The Wicked Witch of the West melts from water, Baba Yaga is weakened if her mirror is destroyed. Witch is also a generic term that can range from "Oz" to "Practical Magic" to "Buffy." It can reference a supernatural creature or a normal, human woman who uses supernatural forces.
So, the penalties or side effects can be as varied.
So, focus on the character and the effect. "The beautiful woman cracks when angry showing a hollow interior"
Honestly, this is "Directing Symbolism" 304. (Third year, major class, because you want some terminology and experience before you start doing in depth analysis). The idea of a beautiful veneer cracking can be symbolic of the beauty being damaged. A veneer can be a false cover. The hollow interior... One can run with that about as far as one can run with Tony Stark having no heart.
I don't think there is a specific "Canonical" reason for it. I think we can basically point to Burton making a directorial decision. And I'd hazard a successful one if it resulted in someone asking, "Why"