There are a few reasons for this. To begin with, number of tears is rarely an accurate reflection of depth of emotion. I think when the pain and sadness are deepest, our heart cries more than our eyes. It's like a defense mechanism. We are able to hide the pain so no one will ask and bring it up again. We can shed almost no tears for enormous amounts of pain. The reverse of this is also evident. There have been many times when I've cried an absurd amount over some tiny thing. This has more to do with where I am emotionally before that point than with what actually happened. Occasionally, of course, our tears do get it right and accurately display the correct amount of emotion. But I think these times are considerably less than we might think. This, however, is only one reason why the expression doesn't make sense.
The second and, I believe, more important reason is that we tend to cry the most because of the same people who make us smile the most. I know plenty of people have done or said some reasonably hurtful things to me. But most of them I just shrug off. I don't really know the person; their opinion doesn't matter to me. But if someone I love and care about deeply says something even slightly upsetting, the floodgates open. This isn't because they are trying to hurt me or because what they did was particularly hurtful. I am just more emotionally invested in these people. What they say and do has greater wait than anyone else. There must be a reason I love them so much, and it definitely isn't because they make me cry. They also make me happier than anyone else could; they love me more and show me that love constantly. Consequently, they have the greatest potential to hurt me. This is why it isn't fair for someone to say, "If you got a penny for every tear you've made me cry, you'd be rich." The tears you've cried over someone in no way means they have been especially terrible to you. Instead, you should say, "For every tear you've made me cry, you have made me smile a thousand times more."
