Pirates bounties are based on their threat level to the world government. Typically there are a combination of several factors that make up a bounty which includes strength, crew, territory, DF, information or knowledge possession, intelligence and more.
Hancock can be a bigger threat to the world government and still weaker than Zoro. She has her own crew, territory, and a hax DF. If she wanted to she could send part of her crew around the world to attack different towns. Zoro could still only attack one place at a time. There's some information the world government doesn't know about Zoro.