So far, so good.
I just noticed this thread today. Everything seems to be working normally for me. I checked the Automatic Ephemera site; this works, and I can see the "https" in the address bar, and on the main site.
I mainly use OSX 10.9.5, Safari 9.1.3, which I know is outdated. I have been increasingly running into websites that do not work properly on this version of Safari, but I cannot update Safari without updating the OSX. So, as a quick fix, i switch to Firefox for problem websites.