The folder in the dock is an alias (Shortcut) to the actual folder.
When you click on the folder in the dock and see the contents, any action you take on those contents is actually taking place on the actual files.
By the way, it is not a Stack. Stack just refers to the way that the files are displayed for you when you click on the folder in the dock. The appearance is customizable. The stacks view really only works well with a folder that does not have a great deal of content.
Just my opinion.
Does that answer your question?
Running Mac Os 10.5. If you delete the downloads stack, does that delete the actual files? Does the same go for the documents stack? Sorry for the dumb question!