> The default structure creates these rather nasty
> names:

Are you mirroring only the PDFs?  You may want to try this structure:

%h/%[fn:pdf/:::]%n.%t

It's ugly but will give you results like the following so at least you can see
the PDFs' code:

c:\www.historicaldirectories.org\pdf\e__hdapps_00009zo0.pdfpdf.pdf