I have the exact same problems!
I was just working on the pictures, creating new folders, etc. And suddenly I realized the pictures went missing - hidden. but thats not the only thing - also the libraries were automatically set to hidden with no option to change that.
And I have no idea why or how and how to change that.
The only two new things today that happened were: Firefox Update to latest version and connected a new Western Digital external hard drive, but actually didnt do anything with it, was just connected.
it'd be great to get some news on this!!!! Thanks