Some attorneys take a position that if a court order determines that an individual is the biological father of the child then no DNA test or John Doe is required. Other attorneys, myself included, take a more conservative approach and assume that until a DNA test confirms the biological relationship between a presumptive father and the child, a John Doe must always be given notice of the adoption proceedings.
Sometimes a birth mother does not know who the biological father of the child is or it is uncertain whether the named father is in fact the biological father of the child. We cannot just assume that a man named by the mother as the father or the man who is named on the birth certificate is the actual biological father of the child. We have to take certain steps to attempt to determine with some certainty who is the biological father of the child.
In almost all cases those efforts are not treated as being successful unless we are able to obtain a genetic test (DNA test) confirming the biological relationship between the man and the child. If those efforts are unsuccessful and the identity of the biological father cannot be determined with some certainty then John Doe is used as the name for the unknown father. John Doe (or another generic name such as Richard Roe) is the name given to the unknown biological father of the child.