There are several things to consider when pruning conifers. Of course these plants are quite different than deciduous plants. We are not always able to see exactly where the buds are, and in many cases there are not adequate adventitious buds below the leave structure. If we are not mindful of those things we end up with one of the most common mistakes made in pruning junipers, even conifers in general. The blindside, often times the backside, or the area within the plant at itself, the area away from sunlight becomes full of deadwood. Prune the deadwood, there always needs to be green wood on a branch.
Another issue — sometimes we don't like the shape of a conifer, some even want to prune it into the shape of a meatball, for example. There is a way to go in and prune so that it looks more natural instead of creating that sheared look. It's best to go deep into the stem and remove it. Then it doesn't look like you have pruned it at all. In this area they have several sections where their limbs that have died out. In those cases go ahead and take the dead wood out. When one doesn't do that it restricts airflow. The area then harbors disease and moisture builds up. Not a recipe for success. So clean the deadwood out. This is an important part of good plant maintenance. If we allow allow deadwood to stay in a plant that is the place were bacteria and fungus can start to grow. It can be harbored there and then spread to other parts of the plant, even to other plants. So cleaning out the deadwood is the healthy way of taking care of conifers.