Annotating increases PDF file size. For example today I got a PDF file which increased its size from 81.6 KB to 3.4 MB.
I assume this to be because DEVONthink To Go embeds the font file several times. See the result of pdffonts before and after the annotation.
This does not happen always, but it’s not rare to happen.
It can be related that I often annotate Japanese text.