Hi jabook,
I have a PB360. As far as I can see you can use the 'Find book' feature to search current folder or all_books for a simple text string contained in filename and/or title and/or authorname. For PDFs that would be filename, so as long as you give your PDFs meaningful names you'll be able to find them.
I can't see a way to search by genre or year unless you have included this info in the filename. There is no Regular expression searching.
I'd just like to reiterate that Calibre is more than capable of searching the way you want, even PDF files (and any other ebook format) and regular expressions. Calibre is also capable of sophisticated naming of files as you send them to the PB (and any other reader) so you can include any metadata you like in the filename. I suppose there may be a filename length limit but I haven't pushed hard enough to find out.
When Calibre is connected to your reader it displays a column showing whether a particular book is already on the reader. So if you ran a complex search on Calibre with the reader connected you would be able to see which of them were already transferred.
Of course, I cannot say what the new PB models will be capable of (one would have to hope they haven't regressed).
If I've got any of the above wrong I'm sure someone will be along to put the record straight.