I don't think that cracking means breaking up in this context. This is a description of Dr Mortimer's voice as he reads the quite lengthy manuscript on the history of the Baskerville curse. It is really not plausible that his voice should be breaking up all through the reading. Although you can say that someone's voice cracks, meaning that temporarily no sound comes out, at a moment of great emotion, that is not going to happen throughout his reading. Dr Mortimer is not an unemotional person, but he is familiar with this manuscript and unlikely to be overcome by emotion while reading it. In any case, this is clearly a description of the general character of his voice, at least his reading voice, not of a temporary, circumstantial change in his voice.

"Crack", applied to a voice, originally meant to what we now refer to as the voice "breaking" in puberty, when the male voice is becoming lower and liable to squeak and change pitch suddenly and uncontrollably. This meaning is already found in Shakespeare; indeed, a youth was by extension called a "crack". I think this may be, at least in party, what the term refers to here:

" 6. to change rapidly in register; of a pubescent boy's voice) - to alternate between high and low register in the process of eventually lowering."
http://anglish.wikia.com/wiki/List_of_Old_English_Words_in_t...

"crack
intransitive v. To change sharply in pitch or timbre, as from hoarseness or emotion. Used of the voice."
https://www.wordnik.com/words/crack

Of course, this doesn't mean that Dr Mortimer was actually a pubescent youth, but simply that his voice had that quality: wavering or fluctuating in pitch.

An alternative interpretation is that "cracking" means "hoarse", that is "rasping", with a harsh sound:

"Physical symptoms felt by the patient include a hoarse, hollow, husky and cracking voice"
http://www.herbs2000.com/disorders/laryngitis.htm

So here I think it's a question of timbre, not of emotion.