Currently (Jabref 4.1), there is no way of using abbreviated journal names in the filename format patterns.
Our import default PDF file link action is currently set up like this:
Filename format pattern; [bibtexkey}
File directory pattern: [journal]/[year]
It would be very nice to have an option here to use the MEDLINE or ISO abbreviated journal name, e.g. by using [journal:MEDLINE], since our current directory structure is set up this way and currently we have to manually move files around during import of new PDFs into the database.