I don't see any reason why you'd really need to get wax from an apiary. But I also don't see why we need wax to begin with. Treat honey as being beeswax with with honey on it the way you can buy raw honey with beeswax at some places. Then just have honey be the requirement to craft an apiary. Requiring another item that you really only need a few of in an entire game and is useless for anything else is kind of dumb.
As far as the rarity, I think it's fine as it is now. It takes time to buy multiple apiaries, but you don't really need a ton of them. One is enough to handle all your infections for 2-3 people or so. You might struggle for a little while after first making one since you might need to use everything that is made initially before you start being able to set some aside in storage. But once an infection is cured, you now get an hour (I think it's an hour) of protection from being infected again, so you don't need to use honey often. If you make 2-3, you should have enough to handle even 8 players. And by the time you can make the honey food (if you even want to bother with that -- I don't), you should already be stockpiling honey if you are grabbing it out regularly and not letting it just sit in the apiaries or forgetting to refill them with flowers.
If they make wax more common, you'll just end up with stacks and stacks of it that can't be used.