Pruning bonsai trees is necessary for a number of reasons other than the basic aesthetic value it provides.
The majority of trees need light and air to maintain good health. Keeping the correct levels of foliage on the bonsai tree ensures that air can circulate around the branches and also allows light into the center of the trees. The lack of these two elements can cause weakness in the affected areas and also make the tree a bit less resistant to fungal infections.
Light entering the inner parts of the branches also encourages back budding (buds and shoots on branches that can be developed into new branches) which increases the quality of the leaf pads and foliage distribution.
Most trees try to grow atypically dominant, the most vigorous growth is on top where the tree can access light better. This can weaken the lower branches if it is not controlled.
Pruning can also help distribute the growth hormones of the tree. If, for example, a tree is left to growth unchecked in one area and the others are kept trimmed then it is possible to strengthen this unchecked area by encouraging the sap in the tree to flow more readily into it.
Deciduous trees are very forgiving with pruning, Pines and Evergreens need more care as a lack of foliage on a branch can reduce the sap flow sufficiently enough to damage the branch itself.
Also the longer a branch is left to grow the thicker it will get which allows trees to be developed. These can then be reduced once they are at the desired thickness. The gap between the leaf nodes (internodal space) also increases which can make trees look 'twiggy' if they are not kept in shape