I found what looks like an ideal solution to keeping beehives in a secure location where building destroyers can't path to them and keeping the fort's beekeeper relatively safe from harm.
Here we have a constructed building with fortifications that has a single beehive installed. This building is completely sealed from the outside with walls, floors and a roof, and the only way in is underground through the fortress. As you can see, the game lists the hive as having outdoor access. I noticed in an earlier fort that bees can fly through fortifications, so I've been wondering if beehives can be safely kept behind them and still be functional. This seems to be the case. When I took the screenshot, the outer bridge that seals up my fort from the outside was open, but after closing it and sealing the fort, the hive still listed outdoor access. I placed a second hive 1 tile south and east of this first one so it wouldn't be adjacent to any fortifications and it also lists outdoor access, but I have a better idea than this construction I have set up.
Presenting the Bee Tower:
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It's simple. Just a 5x5 square with fortified walls, with hives in a 3x3 square inside and stairs in the very center. Since you only want a single beekeeper in a fort with the beekeeping bugs, you only really need a 1x1 stairwell. Optimal output is at 40 hives since production slows down at 41 hives, and with 8 hives per level with this setup, you can stack 5 of these levels on top of each other.