Yes they did. History documents that they did. That is one of the main reasons the indians rose up and threw the Spaniards out of Mexico with a priest, Miguel Hidalgo, leading the way. He himself had an indian mistress and many children by her. Read the history books.
Then he wasn't raping lots of other women, most likely.
Having a mistress or concubine or several has been common throughout most of history, for men in charge.