I did testing annotating the native Evernote Reader(not sure what runs this behind the scenes.) I then opened the PDF I edited in Adobe Acrobat Reader, and the text was clear again! It seems that the original quality is preserved somehow. If I had to guess, some kind of compression has to take place for the annotation function, but I'm not sure. Annotating with Evernote and reading in a different app could be a good workaround for some.