Based on having document names (not only titles) stored in Visual-Meta when creating a reference in Author, and this being available in Reader, the following should be possible:
If the user has downloaded the document which is cited (linked to), and it is in a folder known to Reader (or a sub-folder therein), then the user should be able to click on a citation and the local document should open, not a web address.
- The user has already downloaded the document cited.
- The document name has not changed.
- Can the folder have folders inside it?
- Is it much work for Reader to check if, on user clicking a citation in the document like this  if the document linked to is on the hard drive.