I have the same issue with Endnote 8 and Sierra 10.12.5. Endnote freezes/hangs when clicking on or viewing a reference with an attached PDF with annotations saved to it (Mine are marked with highlighting). The only solution I’ve found is to same the PDF to another location (desktop), delete the reference from Endnote, and then re-import it. Not really practical, but if you only have a few annotated PDFs you are working with, can allow your work to continue temporarily.
Hope they fix this bug soon, its been awhile from what I can see in this thread!