In short, YES you should cluster the service if possible.
I have seen lots of posts on this and I think that some recent problems with SSO clustering (see my post here for fixes) may have caused people to shy away from it. If you are running SQL on a cluster, then you may as well tack on another clustered service and have that much more protection. If you are not running SQL in a cluster then clustering the Master Secret Server will probably not make much of a difference for you!