Doesn't seem like this forum has a lot of high level managers commenting on formations. I hardly consider myself at level 14, a high level manager. Its definitely a very interesting question, and i'm very interested to see where the discussion goes.
Regarding counter-formations, I'd be surprised if they didn't exist. It's based upon the logic of I've had plenty of success playing the counter-formation strategy, so the basis of my system resolves around the theory of counter-formations.
However, this wouldn't stand up to any sort of scientific analysis. To actually test the effectiveness of counter-formations, i'd have to isolate the variable of counter-formations. This means playing the formation that is countered by my opponent's formation, which maintain the others variables (morale, condition, win bonus, etc...) It would also have to span a significant duration of matches to obtain any substantial quantifiable data, so the outlier games against low Q teams, teams with abnormally good or bad form and troll results don't skew the data.