As far as I know these keys could be found on some keyboards that are extinct nowadays. I have to confess to have never seen any other keyboards in real life (save computer museums here) but standard 104/105 ones (as well as localised flavours of it) and Mac keyboards.
I am sure enthusiasts have fancy keyboards with lots of extra keys (possibly, including the keys in question) and it is probably true that computers that are neither PC, nor Mac come with their own keyboards. That being said, all these keyboards can hardly be called mainstream.
All right, Super has a direct equivalent in what they call the Windows key in MS world, but the other two seem to belong to the time long past. I remember seeing instructions with phrases like «Meta is Alt» and in some cases it has been «Meta is the same as Super». Hyper is even more enigmatic beast not unlike Unicorn.
Why are people in *nix world still sticking with these obsolete key names as though they corresponded to real keys? What is wrong with real Ctrl-Alt-Shift-Win(Super) from the perspective of the *nix community? I would like to know if there are any reasons to use these names except for historical ones.