Most commonly the honey is added to recipes once they have come off the heat and cooled down a bit. Is this what you are referring to? In that case, usually the decoction is cooled enough to not be of much damage to the medicinal properties of honey, while still remaining warm enough to mix in the honey well.
Whenever making an infused honey some folks may warm it slightly to strain the herb out more easily or to help with the infusion of the herbs (by placing it in a warmer window, over the fridge or near a wood stove). It would also be recommended to keep the heat to a minimum in this case as well. Perhaps not much more than body temperature for example.