I was always under the belief that Anse knew but chose to remain silent. The very fact that Jewel is so extremely different from anyone else in the family is enough to put his parentage to question. Plus, Jewel is Addie's favorite, and she makes no bones about it. Addie is not one to go back on her promises...she is as stubborn and single-minded as all of her children and Anse (they all have a reason to go along on the ride to bury their mother/wife aside from the funeral itself). However, that being said, I believe that she and her husband restored relations as a peace offering for Addie's betrayal. Thus, Dewey Dell and Vardaman exist.
It seems to me that we can look at Jewel as being a product of Anse's stubborn insistence on "not doing for himself."
Whenever he can get help instead of doing work, Anse will get help. How long has it been since he broke a sweat?
I don't know that Anse would be upset knowing who fathered or didn't father Jewel. The idea that Jewel is someone else's son works to allow Anse to righteously suffer (which he really likes to do) and it gives him the right to beget more children (however strange the process of earning that right might seem).
I think that Anse is aware of Jewel not being his child, and responds with his typical inaction. I think that they produce Dewey Dell and Vardaman as a couple as more for Anse to divert attention from Jewel back to himself than a restoration of amity between husband and wife.