Answer
By creating a test area with a variety of saplings that is not affected by the deer, which can then be compared to the areas in which deer feed.
Work Step by Step
You could do this by planting saplings in areas the deer could not reach, or by restricting the deer's access to an area. In either case, the test area would need to be otherwise identical to the areas with deer grazing. The only difference would have to be the presence of feeding deer.
Even in this case, however, it may be difficult to determine whether the cause is specifically that the deer are preferentially eating the saplings. It could be some other impact of the deer that prevent them from growing, such as their treading on the ground around them, or the affect of their droppings in the soil. Further observation and potentially experimentation would need to be done to determine that it was preferential feeding specifically causing the change.
