I had the same problems.
I don't have that many documents, but I do take a lot of notes on PDFs. I archive my annotated PDFs on my PC, but I wanted to keep a backup copy of all the archived files on an SD card.
With about 200 PDFs and roughly 2,000 notes, it takes about 20-30 minutes to finish loading.
Even worse, if I try to add notes to any document, it seems to take forever to save them.
Both problems disappear if I take the SD card out.
I don't really care about carry THAT many documents with me (although, SONY lying to us once more - I got burnt on TVs, PS3, cameras, etc. - does piss me off). But I would like to have a way to backup my annotated files, in case my PC crashes.
I tried copying the SONY database on my PC, but once I transferred the files to another system, I couldn't access the notes. So I resorted to the SD-card method.