Yes, almost Werewolves have souls since they are still human by day, and on the nights devoid of a full Moon. The human soul is still connected to them even in Werewolf form. However, they are not held responsible on a Heavenly level for any atrocities they commit in their mindless monstrous form. This is somewhat on the same level of mentally ill individuals being exonerated of any crimes they committed while psychologically impaired. That is unless they have mastered the ability to remain cognisant once transformed within the silvery lunar light.
Interestingly enough, there is one variety of Werewolf with no soul. If two Werewolves mate in their furry form then they will produce a rare pure blood albino Werewolf devoid of human form, and a soul as well. It remains a Werewolf 24 hours a day. It is a pure demonic abomination! Thankfully, such monsters are rare due to most lone werewolves attacking each other. Only under certain moons with sensual influences does this happen. Those who can keep their human wits about them in werewolf form know better than to create such a hell hound!