Recent mac update - Update 10.12.5 partly fixed the problem.
Strange thing is that for couple I had native EndNote PDF reader but now disappeared. Double click on reference in the past would open native Endote PDF reader now it is opening reference editing. Native endnote reader disappeared and documents annotation can either be done only in Preview or Acrobat Pro if you have one.
However, it is still buggy and freezes but less than on 10.12.4