After some IRC-based investigation, Rich Trouton has a more definitive explanation for the cause of the mysteriously-disappearing
/Users/ folder. Turns out it’s not the 10.9.3 update as previously assumed:
After considerable investigation by the folks in the ##osx-server IRC room, it looks like the issue has been tied to two causes:
iTunes 11.2 being installed
iCloud’s Find My Mac being enabled.
The 10.9.3 update does not seem to be the root cause, as the behavior has also been reproduced on 10.9.2 with iTunes 11.2 and Find My Mac enabled.
If anything, that’s even more bizarre than a 10.9.3 update-based bug. Trouton has an even better workaround for fixing this bug.
(Thanks to Anthony Reimer for pointing me to this article.)
Update: Apple has now fixed this issue by releasing iTunes 11.2.1.