Depends on the type of undead.
From The Great Beyond: A Guide to the Multiverse:
Souls have a complex relationship with the state of undeath. Unintelligent undead, for instance, are shells of creatures who formerly possessed souls; however, these undead do not have souls of their own, and are little more than automatons animated by negative energy. Intelligent incorporeal undead, on the other hand, are the physical remnants of souls without bodies who refuse to leave the Material Plane. Still other undead, such as intelligent corporeal vampires and liches, are material bodies that possess mortal souls twisted by negative energy.
So if you’re talking about skeletons or zombies or similar unintelligent undead, those souls have flown the coop. Soulseeker will show you the way to their souls just as it would if you cast the spell on a regular dead person.
Intelligent, incorporeal undead are souls (or the remnants of souls) that have not moved on. Soulseeker, if you cast it on the material plane, should guide you to the ghost, banshee, shadow, etc. of a person if that’s what became of the person’s soul.
Vampires and Ghouls and other intelligent and corporeal undead still have their souls. Liches are a special case because while they still have their souls, the do not keep those souls inside their bodies, they keep them in their phylactery. A GM might allow you to use Soulseeker to find a Lich’s phylactery. If one adheres to the strictest letter of the rules, then Soulseeker should guide the caster to either the physical body of the undead who still has its soul within it (like a Vampire), or to the phylactery of a Lich who keeps its soul there. After all, intelligent corporeal undead are not alive, and therefore the spell should not fail when they are its subject.