I need to bake this model for a game, but there are lots of small cylinders. If I join all the objects, the bake comes out with lots of black spots. Do I have to manually bake each object or is there an easier way?
I suggest you to "explode" the geometry and then bake, explode means; you take everything apart so there is a margin between they, you have to do this for every pass except the ambient occlusion pass
-separate the pieces when there is a weird angle(not sure of this last pàrt)
Supplementary: this video shows the process done in maya and substance painter, but its the same for blender https://www.youtube.com/watch?v=3fY3LEnoRxU&t=7s