Can they issue a warrant on you if they cant find the vehicle?

Yes. Your question does not make any sense, but yes. A warrant for your arrest can be signed at any time with sufficient cause. A better question is why do you think your getting a warrant and how is it related to this vehicle. You filed under repossession, and to my knowledge you cannot get a warrant for hiding something from being repo'd. They are separate schools of law, the repossession being under a breach of contract between you and the loaning institution (contract law I think its called), and a warrant would be regarding criminal law.