First, your in-depth posts have provided me with invaluable information about my phone and its development; thank you!
This may be a totally uninformed question, but I have been trying to follow your posts and wonder if 1. the version does matter, and 2. does the method of update matter? My version of 9.3 is 9.3 (13E234). I updated the day the update came out via the phone (6s plus) through General, Software Update. The link issue did not occur immediately, but only on Monday, just after someone sent me a text with a Flipboard link about the problem. I was able to follow the link and read about this issue, but ironically, when I went back to the text to sent the link to someone else, it froze. Then my native iPhone mail app crashed with any links. I have tried the JavaScript and all the other early "work-arounds" to no avail. My only saving grace is that I also have a Gmail app, where I get most of my emails, and those links go to Chrome, which works fine. Prior to this issue, I have had intermittent problems sending and receiving mail outside of the home wifi, particularly Gmail, which is why I have the app, as I can't trust the native mail app to get my email. Those mail issues got considerably worse after the 9.3 update. My husband has the identical phone, but he updated through iTunes, and has no such link issues. His version number is also 9.3 (13E234), and he did log into iCloud during his installation. I also updated his very old iPad to 9.3, but DID NOT log into iCloud during the install, and it has no issues. So, I am just providing this information for your impressive research, in case you think there is any bearing on the particular version number, or the method of install.