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You can still access the pdf file via the file system by right clicking on the item and 'show file'. The files names may not be user friendly though.

There is handy functionality to rename pdf files based on parent metadata. I think you can set this up to be done automatically on import too.

This is great to have consistent filenames from lots of different sources. Of course if the metadata is wrong or missing, it won't help.

zotfile plugin, mentioned above in this thread, makes file names user friendly.