We know that Brando chose the high raspy voice after he heard tapes of a Mafia hearing.
But usually such a voice develops with vocal fold nodules (In the case of Johnny Fontane, Jules called them "warts".) And you get them when you yell a lot, or cough and speak at the same time.
Vito was a quiet man who rarely raised his voice. Now, I'm not saying, it was a bad decision by Brando, but I've always felt that a sonor voice would have suited him better.

A guess is that Brando, trying to get into character, imitated the raspy voice of Frank Costello. He was the only Mafia Don of his era to appear on televison, during the Kefauver Subcommittee hearings (1950-51). The heariongs were viewed by tens of millions of Americans; and, although Costello's face was not shown (he permitted only his hands to be televised), he was on camera for hours.

I can't imagine Don Vito talking any other way..

I agree.

and yet, he had such a beautiful, angelic voice as a child... What the hell happened that his voice would become so raspy by the time he was 25?
Smoking? Was he hitting the opium dens? Did some punk punch him in the throat and ruin his vocal chords in his teen years?

So sad that he never sang again...

Maybe he did sing as a teenager, but it's something the viewer didn't need to see. De Niro perfected the young Vito role.

Puberty