While having beehives for each woodset could be a good idea it's also quite bloaty, like how quark having chests for all wood types adds lots of extra blocks

Could it be made configurable so that if you disable the beehives, they don't appear in-game + aren't craftable?

Currently disabling the recipes in the game is impossible (it would require restart) and it would also require a lot of work, since now its just a datapack adding those, so nothing like this is planned at the time, sorry.