I am playing on PC and sometimes the waymarkers and other quest markers dissapear. I then have to look on the Map if I am going the right way. In my first person view I don't see them. Sometimes they suddenly come back and later they are gone again. Is this maybe a key that toggles this?

I believe “y” might toggle them.

There should also be an option in the HUD. 

If that doesn’t address your problem, then please know I have had them display so high in the sky that when I looked around me at ground level I could not see them.  You might be experiencing that glitch.

Thank you very much. The "Y" does the trick!!