As soon as tags are accessed from Lua, they are processed by the MediaWiki software and the reference will appear in the reference list at the bottom of the article. If your module proceeds to omit the reference tag from the output, you will end up with a phantom reference - a reference that appears in the reference list, but no number that links to it. This has been a problem with modules that use to detect whether to use the arguments from the frame or the parent frame, as those modules automatically process every available argument.