Encrypted swap (and hibernate) continues to work for me on Ubuntu 16.04. Granted I set it up a while ago, but that was the procedure I used.
I don't see anything upstart- or systemd-specific with those instructions... Did you set up "regular" encrypted swap (using ecryptfs-setup-swap) before starting? Did you follow the instructions exactly (especially step 8, editing /etc/crypttab)? What do you see when your computer boots?
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