it was a tough call, I went back and forth on this particular item.. on the one hand, I would expect it to work as you do, if I have a category of cars with sub categories of Ford and Chevy and there are 2 entries in Ford and 2 entries in Chevy, then I would expect to see 4 as the count for cars. However, on the other hand if you look at it like a directory there aren't any entries in cars. If those were folders on your hard drive, a root folder of cars with sub folders of Ford and Chevy and looked at the properties for the root folder Cars, it would say the file count was 0. There would be 2 sub folders, but the item count in the root would be 0.
I opted finally to implement it under the folder paradigm, but I can see how it doesn't meet every use case. I suppose the best option would have been to make it configurable in the module settings, or implement it in the .xml settings file for the dashboard as to whether or not you want category counts 'rolled up' to parent categories.
If I have another 3.X release, I'll definately try and implement that option. Right now, I'm starting to work on the 4.0 release and don't really have plans to release another 3.X based update .. but who knows :) worse case, I could always blog about how to implement it yourself if you're feeling frisky