Not necessarily, being in prison doesn't automatically mean you lose parental rights. The only time it really happens automatically is if the victims of the crimes are the kids. I do foster care and a lot of my foster kids have parents in prison who don't lose parental rights.
Adoption for kids who've lost a parent is generally not the best route for them in most cases, legal guardianship is.
Kids' who have lost a parent have lost enough and adoption takes away that legal connection to them. When you're adopted a new amended birth certificate, it removes the biological parents names and replaces them with the adoptive parents names.. like their parent never existed in the legal aspect. When they get married, apply for a passport and things like that it asks for your parents names, at that point you have to put down your adoptive parents names, not your biological ones ... it may not sound like much to you, but it does to an adoptee or a child who lost their parent.
Before anyone could adopt them though, they need to be free and clear for adoption meaning their fathers parental rights are terminated, either voluntarily or involuntarily.