There must be a middle ground somewhere.

On one end we have the enlightenment rationalist, who are all too sure about their beliefs, who are arrogantly certain about any and all issues under the sun. On the other end we have those to claim all too much is mysterious and forget that God gave us brains to exerise wisdom so we can understand things.

There are also many who claim mystery for issues when really they just have an incorrect or inaccurate understanding.

I think many times when Paul uses the term he does NOT mean the issue is unknowable, but rather that the issue is very profound, complex, and perhaps unanticipated. The cross and the church are both issues Paul calls mystery which would fit this category. We might not every be able to fully grasp the whole truth, scope and implications of these issues but we sure can know some things about them.