Can I use self leveling compound to level old thin set over plywood subfloor?
Yes you must remove all of the thinset - FOR SURE.  Thinset is not meant to be exposed and a leveler on top of it will not protect it enough.  From walking and moving furniture you will end up with chunks of thinset/leveler and it will just be a mess.  

You either have backer board or plywood under the thinset.  You have would really grind off thinset in this scenario but you can:


pry up the first layer of subfloor and redo it.
try to hit it with a heavy scraper.
and what I would try first... pound it out.  Most thinset will disengage with heavy vibration.  Try a hammer or mallet on a small area.  Strike the thinset repetitively pretty hard in a circle pattern.  See if you get some chunks disengaging after the first few minutes.  If this works it get much easier after you start.