The way I've heard it described (and I think this is a decent way to look at it) is that with hitters, ratings like contacts and power indicate how successful a hitter would be against a pitching machine. So if they saw nothing but straight fastballs down the middle, a 100/100/0/0 hitter could still belt it out of the park every time. But against an actual pitcher, that hitter would be lost. The effectiveness ratings dictate how well the hitter can put those skills to use against an actual pitcher of that type.
The same could be said of pitchers, though it's a bit more abstract in my opinion because of the values of the other ratings; if a guy has 100 control and 100 velocity, he can put the ball anywhere he wants as fast as he wants and usually this alone is the makings of a Hall of Fame pitcher. But in HBD, it's different-- for whatever reason, even having perfect abilities won't allow you to dominate hitters unless you have good effectiveness ratings against them. In this ragard, if you offered me a pitcher with mediocre control and pitch ratings but 100/100 effectiveness ratings, I would much rather take him than a guy with 100 control and great pitches but effectiveness ratings of 35/35. Maybe it's an ability to "fool" hitters, to hide your pitches, to throw them off with your motion... I don't know what effectiveness could be likened to for a pitcher. All I know is it is virtually impossible to be a good pitcher, no matter how good your other ratings are, unless your effectiveness hits, say, 50. And even then, I prefer not to go under 60, and that's with a guy with great control and pitches. 70 is more my comfort zone and 80 is Cy Young caliber with other good ratings. 90's are a special breed if you can get them with good control and pitches.