There is no specific option for excluding a folder, except of just not including it in the path. WED resources only the files that are used in the level or in the script. Files not needed are not resourced.

When a file intentionally must not be resourced, but is used in the script, it can be excluded via extension or file name. If it is needed and not excluded, WED will produce a warning when the file is not found. I know no way to disable the warning.