After the winter of 2010 my hedge started dying and now the spots have become...
We assume your shrub is a Japanese holly. Both Japanese holly and boxwoods tolerate heavy pruning and your shrub would benefit from extensive thinning. You could even cut them back to a foot or two above ground and allow them to regrow. This would allow you to train them as they develop.
The dense growth prevents the sunlight needed for healthy foliage. Also, good air circulation inside the plant is necessary to prevent fungal problems.
You could prune out dead wood now, but wait until early spring if you decide to do renovation pruning.