Your sauce mellowed. I always advise people to try their bottled sauces a month later. They will taste different, so if you want to know how customers are going to taste your sauce, after sitting on a shelf, then you can't judge it right after you make it.
No, sugar does not neutralize capsaicin. It displaces it (removes oils from tongue, like milk, but not as effectively), and then it is swallowed. So, if it's in the bottle, there is no displacement. Where would it go? Nothing neutralizes capsaicin chemically, but there are ways to relieve the sensation, and just barely.
The honey did not kill off heat. Your sauce mellowed after aging. Flavors melded and capsaicin was absorbed into some of the ingredients, etc.
You know how marination works? It is similar, and your sauce has now marinated. Chunks, even small ones, have absorbed liquids, chemical things have happened, etc. etc. It has become one.