Most – but not all – folks who upgraded to 10.9.3 yesterday immediately began noticing that their /Users folders had disppeared. Those who looked also found that their /Users/Shared folders had disappeared.
Never fear, we published a few tricks to unhide those folders.
We became curious when more and more people began reporting that their folders hadn't disappeared, so we set about doing some isolation testing. After all, OS X 10.9.3 wasn't the only update Apple released yesterday. iTunes 11.2 made its public debut, as well.
Turns out that hidden /Users folder has nothing to do with OS X 10.9.3. Your /Users and /Users/Shared folders will be hidden by OS X upon every reboot of your Mac if you have updated to iTunes 11.2 and have Find My Mac enabled.
This hiding of the /Users folder happens at reboot, so it's possible to still see it even after updating iTunes with Find My Mac enabled. Once you reboot it will disappear. Even if you use our trick above it will still disappear after you restart your Mac.
Once it's hidden it will stay hidden, though, even if you disable Find My Mac and then reboot. However, if you disable Find My Mac and run our Terminal command in the aforementioned article, the folder will stay visible.
One of our readers indicated that Apple said this is intentional. If it were in 10.9.3 I would believe it. But seeing as how it's related to the iTunes update, I'm not sure. We'll reach out to Apple and let you know if we hear anything official.
[Update: iTunes 11.2.1 fixes this issue entirely.]