Like Jayden said, paps aren't testing for warts. So having a clean pap does not really have anything to do with having warts. The only way your doctor would know if you had warts is if she saw them during your exam. So if you had them during your exam, and they are noticeable, it does seem like the doctor would have said something. Either way, I would schedule another exam if you have to and ask about them.
For future reference, there are all kinds of STDs that people can have without showing symptoms. So never assume that if your boyfriend looks clean, he is clean. Looking clean has nothing to do with being clean.