If its using cm11 there was a bug where app icons would disappear from the launcher after app updates.
Apps uninstalling themselves though... Besides user error or bad judgement I can think of many possible scenarios where apps could be removed/disappear.
I wonder too if google's new app checker service improvement could remove them if it didn't like them. Perhaps even being triggered during an automatic update.
[Ah yes, there is what I was looking for: "Google Play scans apps that are uploaded for malware. If an app is later discovered to be malicious, Google can automatically remove it from the devices it’s been installed on." -> http://www.makeuseof.com/tag/cracked...e-downloading/
And that is only one way it can happen.]