If my sons dad is not on his birth certificate and has not been in contact for 6 weeks what rights does he have and would he be allowed contact. He also has a history with drugs

He has, more or less, the same rights you do. The only thing a BC does is to make it easier to prove that he has those rights.

Is there a custody agreement, Is there a child support agreement ?

But in general he has the right to file in court for visits. Since he is not on the BC he will need to prove his paternity by a DNA test.

So you were sleeping with him when he was on drugs, He was good enough to sleep with, not good enough to be the father ? The court will ask about the same question or his attorney will.

Next can you prove the drug use in court, is there a history of his arrests for drugs, Since just you telling the judge is not evidence.

But unless you can prove he is a risk to the child, of course he will get visits, and normally over night visits. Even if he is a threat to the child, he can normally get supervised visits.

Also 6 weeks is really no time at all for no contact, he can come back after a few years and still get visits.