Empty folders with mangled names being put in my user directory
That is one of the strangest things I have ever seen and my introduction to Macintosh was with System 4 on a 512K Mac.

There could be a number of things causing that. A runaway/damaged process running in the background seems the most likely, but I suppose there could also be some disk corruption.

I would boot the system into recovery mode and run a repair on the startup volume using disk utility. If it finds no issue then it is more likely that it is a runaway/damaged process of some sort.

Booting into safe Mode (Hold Shift while starting up the Mac) will disable 3rd party applications that run at startup and if the problem goes away in safe mode it is something that was installed on the Mac that is now damaged. uninstalling the application, turning off any login items (system preferences > Users &amp; Groups > [your user] > login items) and looking for other things that run at startup are a place to start.

If it is still happening it is likely an issue with macOS. In that case you could try downloading and installing the latest combo update, the latest for Sierra is here.

Failing that I would reinstall macOS right over top of what you already have. While that shouldn't delete any data I would make sure you have a good backup first.