Obviously I haven't highlighted or taken notes on pdfs on my Kindle, as that function won't be available until the K3 comes out.
I have taken really extensive highlights and notes on some of my mobi books (.azw format) however and have not noticed any slowdowns in processing. But by really extensive I mean roughly a hundred and thirty notes in a single book. I don't think I approach your total number of notes. I might have 200 or so but not more than that, I should think.
I hope this was helpful.
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