Despawns, or gets destroyed? Have you seen it despawn?

Is it possible a mob spawned, wandered over and killed your beehive, then despawned? Just because you're not there doesn't mean mobs aren't trashing your stuff.

Dropped items get cleared every so often, even in singleplayer... so if you haven't been to where your beehives are in a while, then it's entirely possible that it got smashed and then the bits were cleaned up by the "server".