If you use Skyrim 3D Trees this will fix your beehives. My preference is to hang the beehives from a horizontal branch as I think it looks more natural than the "glued to the side of the tree" look that vanilla Skyrim often uses. However, this was difficult to do with Skyrim 3D trees as most of the tree models, particularly the pines, have very few low branches. In some cases, the low branches or broken branches don't start until almost halfway or 2/3rds up the trunk of the tree, which would put most of the beehives out of reach of a player standing on the ground, requiring the player to knock them down with a ranged attack if they wanted to loot them. So in many cases I have kept the beehives attached to the side of the trunk but rotated them a little bit so that nubbin on top of the beehive isn't just sticking out into the air like a little beehive stovepipe.

Skyrim 3D Trees is a bit of a different tree mod compared to others because it not only replaces tree models but in some cases entirely changes tree types; for example, changing an aspen into a pine tree. I have maintained the tree type files according to what the vanilla tree is that was in that spot in case you use a different aspen mod, or reach tree mod which reverts those tree types back to their original state.

Requirements
This mod requires Base Object Swapper.

What beehives are fixed?
All vanilla beehives and vacant beehives that are supposed to be attached to a tree. There are several which hang from cave roofs or structures that needed no adjustments. Mod-added beehives will not be adjusted by this mod and would require their own BOS file patch. A patch for the three beehives added by Cutting Room Floor is available.

Will you do other tree mods too?
Maybe! Some of them might not need adjustment if they are close in size and shape to vanilla trees. If you use a different tree mod and you have floating vanilla beehives, let me know in the comments which tree type they are floating on and which mod. Check the stickied post for additional tree mods that are done.

I installed a file and I still have floating beehives!
I tested all files on a new game and all of the beehives moved to the appropriate places. If you still see floating beehives, make sure it's installed correctly, and you're not getting an error in your BOS error log, or you don't have another BOS file or mod touching beehives (texture and/or model replacers without a .esp are fine). Also, if you have a mod that changes the treescale beyond what is in the base mod, or have manually changed treescales, the beehives will no longer align. These files can be installed/uninstalled on existing games with no issues. If everything is installed correctly, open the console, click the misbehaving beehive, and type in "recycleactor" which should force it to the correct position.

Can I combine the BOS files I need into one file for my game?
Sure can!