So far so good, I've upgraded to Sierra and have been using a zfs-based home folder for a few days now with no issues beyond occasional minor slowdowns... I have found only a single rather small problem, maybe it's an easy fix, maybe a clue to some potential improvement, so here it goes.
The LaunchPad doesn't display any applications from the ~/Applications folder if the home folder is on zfs. It works correctly for users with their home on the root fs in /Users.