That is a more complicated story than those links suggest.....There is evidence, from the Andrew Hogan book "Hunting El Chapo" that details him procuring sex workers, very young, from picture sent over intercepted BB communications. The DEA agent says as much, but there is nothing about drugging and raping minors. That doesn't mean it didn't happen.
The main witness who alleged those acts is Alex Cifuentes, who is a documented liar, and believes in witchcraft, the Illuninati, alien conspiracies, and the occult. So, that doesn't mean he was lying about this. But, the allegations are a common smear tactic against drug cartel members, apparently. And Cifuentes, had some sort of falling out with Chapo, after he left the witness stand he gave a sign in Spanish for "You just got screwed"/I screwed you".