NOTE: For a word of god answer, see Skooba's answer here.
Begin my speculative answer.
There's no example of a naturally bald Khal in the canon so we cannot draw on precedence.
As far as the implications such a condition would have on his status as a Khal, I believe it wouldn't be much of a problem.
Dothraki follow strength, not hair. That's the only thing they look for when choosing a leader.
The hair's importance is merely that it indicates how many battles has that person won. But it is not the only indicator of a Khal's strength and victories. The number of cities he razes, his personal wealth, the number of horses in his herds, the size of the Khalasar surrounding him, they all indicate his strength and victories. As long as they are sufficiently impressive, I do not see why his hair would be a problem.