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There may a slight increase if you do hundreds of notes, but I just double checked and inserting a highlight at page 200 in an EPUB book with about 50 other highlights only took only about 4 seconds to go from marked to highlighted when you hit the highlighter icon.
The only PDF file I have currently loaded is the Sony user guide, but I did do a quick check of a single highlight at page 125, and got about 3 seconds.
I am not sure if LRF format would take longer, but I would guess that annotations are probably faster across the board, if nothing else, because the processor is faster on the new readers.
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