What are the specific apps? If they are ad blockers then it makes sense, because those obviously have to grub around in Safari to do their thing, and it is easy to imagine that could cause some breakage that makes links stop working.
FWIW I updated my 6s plus the day 9.3 came out, and I'm using an ad bocker (of the dozens now available) and have no problems. Though I rarely use Safari on my phone so I had to check to see if it had broken!
Biting the hand that feeds IT
