In the 12 month reports as well as everywhere else in the game, Honey only counts as being “produced” if a farmer brings it from an apiary’s storage slot, to a storage building.
However, if the settlement has very few farmers and/or they are busy tending the crops, then a trade center employee may grab the honey directly from the apiary and bring it to the trade center to sell.
In this last case, none of the graphs or numbers in the game account for that amount of honey having ever been produced, which leads to confusion.
This situation is especially common in the early game where the only use for Honey is to sell it, and players often configure the trade center to store 500 units of honey with “Keep In Stock” turned on, which takes many years to fill. So during those years the graphs show very irregular and small numbers for honey production even though wax is being produced just fine. And when the Trade Center finally gets full with 500 Honey and all the honey has to be grabbed by a farmer, only then do the graphs show a huge jump in produced honey, even though no new apiaries were constructed. If the 500 honey is then sold to a traveling merchant, and the trade center is empty again, then the situation reverses and the graphs show almost zero honey being produced yearly again.