A picture's worth 1000 words, my canopy diminisher farm:

Honestly don't know why the nests are spawning without flowers around. it's like they're using the worldgen spawn rules when the saplings grow. But if the canopy diminisher could absorb nests as well, that might be a nice feature?

Would you be able to test if this same thing ends up happening without any other mods installed? I'm suspecting that there's a mod in your pack that causes bee nests to spawn even without flowers around.

Closing due to inactivity. If you're still experiencing this behavior, please open a new issue in the future.