Case Status: Case closed. The Amazons took the law into their own hands and made war on Theseus and Athens. Unfortunately for them, Theseus and his army kicked their butts, and they had to go home without their Queen.
Addendum: Some claim that it was actually Antiope, Hippolyta's sister, who was kidnapped by Theseus, which might make sense if Hippolyta was actually killed earlier by Heracles. It's a little confusing, we know.