I have
read about this before and there are at least a couple other explanations besides "bonking a lot of women." In addition to having hundreds of children (which is possible), consider these other factors that may have been in play:
One is that the planet (or even SE Asia) suffered some population declines between 1227 and modern times (Black Plague anyone?) and Khan's descendants, either through genetics or position in life, were better suited to survive the hourglass of winnowing population and pass on their genes.
Another is that Khan (and his descendants) purposely winnowed the pool of sperm competitors.
Related, Khan's descendants could have been more successful, collectively, over a number of generations. Not hundreds of children, but dozens of children by dozens of brothers and hundreds of sons and thousands of grandsons.