Many comb honey producers use smoke sparingly and some forgo it altogether. In Honey in the Comb, Killion notes that “Heavy smoking may cause soot particles to adhere to the surface of freshly capped comb.”
Heavily smoked bees may also rip open capped cells in order to scarf down honey reserves quickly. I’ve seen smoked bees open a half-dozen cells in one square section. That may not seem like a lot, but when you are trying to produce perfect comb, it can be heartbreaking.
In addition, some folks can definitely detect a smoky odor in combs that have been smoked. This varies with individuals, and some are much more sensitive to it than others. Recently a beekeeper told me that his parents’ comb honey always smelled like smoke. Even if you don’t notice it, others may.
So my advice with smoke is simple: if you must use smoke to harvest comb honey, do it with a light touch. Use as little as possible, as infrequently as possible.
In my opinion, products such as Bee Go, Bee-Quick, and BeeDun should be avoided as well. Bee Go is made of butyric anhydride, has a nasty smell, and is both toxic and corrosive. The latter two use herbal extracts and essential oils to repel bees, but because they are oil-based compounds, they can taint the wax combs. Water-based honey will not readily absorb the odor from these products, but beeswax can. Much better to use an escape board and a little patience. Good things are worth the wait.