Anyone else has this issue? What can be done to fix that?
I had the same problem. I looked in my keychain and there were over 500 copies one of my certificates, and a few others were duplicated a few hundred times. I removed all the duplicates and kept just one of each, and my code signing time went from 30 seconds per framework down to about 1 second per. I don't know how the certificates were duplicated, but the timing of the issue suggests it was due to updating Sierra to 10.12.1.