Dealing with low-information centroids using Nearest Centroid Classifier and bag of words method
This is a standard problem with distance/similarity measures between texts of different length. I'm not aware of any standard way to solve it, but in your case I would simply try to remove any email shorter than a certain length from the training set (you can experiment with different thresholds). This would hopefully force the centroids to be more specific, the goal being that none of them can easily attract all the instances.