There is no reason why a hermaphrodite animal should not be sacrificed, unless that affects the quality of the meat.
The Messenger (peace and blessings of Allaah be upon him) described the faults which make an animal unacceptable for sacrifice. They are: obvious one-eyedness, obvious sickness, obvious lameness and extreme weakness.
By analogy, this includes faults that are similar to these or worse, such as blindness, a limp or having a leg cut off. This has been explained in the answer to question no. 36755.
Is seems that a hermaphrodite does not have any of these faults, unless the quality of the meat is affected.
Al-Nawawi (may Allaah have mercy on him ) was asked about sacrificing a hermaphrodite cow and he ruled that it was permissible, as was narrated from him in Mawaahib al-Jaleel (3/239).