Langstroth bee hives are designed to be modular so you can expand the hive when need, and also so you can pull them apart if needed to remove honey or do other things such as adding food for your bees. Since bees add propolis (bee glue, or bee caulk) [https://en.wikipedia.org/wiki/Propolis]bee glue, or bee caulk to any joints or gaps in the hive to help seal it, you don't need to worry about the rain getting in through those gaps. If you are worried about the exterior of the hive getting rained on, lay a large piece of plywood on the top of the hive so that it forms an overhanging roof that prevents rain from hitting the hive.
If you were to cut a rabbet joint into the top or bottom of a hive module where it fits into other parts of the hive and then the bees added propolis to that joint, it would become almost impossible to separate those hive modules without destroying the hive. If you do any woodworking you know that a joint and glue bond forms one of the strongest joints possible, which is good when making furniture but not so good when you need to open the hive.
