Due to time restrictions i'm taking the easy way out :(. If anyone can answer better then what i have i'll gladly choose their answer over mine.
To make the criteria api recognize that i'm looking for the inherited table i changed my query code to be:
CriteriaBuilder criteriaBuilder = entityManager.getCriteriaBuilder();
CriteriaQuery<Car> criteriaQuery = criteriaBuilder.createQuery(Car.class);
Root<Car> car= criteriaQuery.from(Car.class);
Root<Soccerball> soccerballs = criteriaQuery.from(SoccerBall.class);
Join<Car, Trunk> trunkJoin = car.join(Car_.trunk);
Join<Trunk, Ball> ballJoin = trunkJoin.join(Trunk_.Balls);
criteriaQuery.select(trunk);
Predicate [] restrictions = new Predicate[]{ criteriaBuiler.equal(car.get(carModel), "Civic"), criteriaBuilder.equal(soccerball.get("numberOfKicks"),20), criteriaBuilder.equal(soccerball.get(SoccerBall_.id),car.get(Car_.id))};
criteriaQuery.where(restrictions);
TypedQuery<Car> typedQuery = entityManager.createQuery(criteriaQuery);
Car carWithSoccerBalls = typedQuery.getSingleResult();