I'm sure they'd have at least theorized the existence of queens, even if they'd never seen one. After all, I highly doubt Ripley was the first person in the universe to ask "so who's laying these eggs?"
The question would then be how to test that theory and hopefully obtain one. It's possible that the researchers deemed the aliens too dangerous, too rare and/or too valuable to gamble on unleashing them within a less restrictive environment just to see what would happen. Thus, no queens.
What sayeth SM?