If your baby daddy has a warrant and he shows up at the hospital and sign the birth certificate and some one finds out could they take your baby away for that?

Well technically yes. If the man is in trouble for say a violent crime then letting him near a new born baby without the means to defend themselves is putting the life of the child in danger.

If he is not in trouble for a violent crime you still have defied the law by not informing someone that you know the whereabouts of the man. For this you may be deemed as an unfit mother. Since you may not be able to instill in the child the code of Law and Order.