Unfortunately this is one of those areas that history cannot answer. The Spanish were certainly more lenient or liberal than their Anglo or French counterparts when it came to illegitimate children, as mixed-race children often were. The Spanish had a caste system that effectively kept mixed-race couples from openly flaunting their relationships, but Spanish men could and did acknowledge children by their colored mistresses.

Children of rape are harder to estimate simply because of a lack of documents. Men might acknowledge a child produced from rape, but it was unlikely unless perhaps the mother was a slave and the father/master chose to ultimately free the mother and/or child. Since rape is notoriously hard to prosecute and document, it's even harder to estimate how many children might result from it, especially in an age where women's rights were lesser than they are today. And then there are power relations to consider... Even if a man didn't physically force a woman, she might have felt compelled to submit to him anyway because of any number of reasons.