At this point in the novel, Paul has two issues - first, he is the son and heir of a Duke; second, he is a young man.
Dukes are not your average guy off the street, they are very near to the top of any system of nobility. People with that kind of power and wealth (because where there is one, the other generally follows) are not shirking violets. Even the best of them are proud, confident, even arrogant.
Young men, despite their inexperience and naivete, often carry their own forms of arrogance as an absolute conviction in their own immortality and knowledge.
Paul, in his arrogance, does not believe that the Reverend Mother has anything useful to say. His reply "Hint then" is mostly a challenge to her to prove him wrong.
The Reverend Mother is very familiar with the shortcomings of both nobles and young men. She recognizes the arrogance behind his challenge and calls him on it. Her question is both a cautious and diplomatic rebuke, and a counter challenge. She knows the value of what she is about to say and is challenging him to recognize its wisdom and to make use of it, when the time comes.
The possibility that Paul may be the Kwisatz Haderach is too important to engage him in a confrontational manner. He isn't likely to listen to her now, but if she handles him correctly, what she says will be like a seed planted in the fall that will sprout and grow in the spring.
The hint itself is actually a common theme in human art and literature, going back as far as the New Testament of the Bible, where Jesus said that last shall be first. It appears contradictory on the surface - and perhaps from a pure-logic point of view it is contradictory - but it comes from the purely emotional side of human nature that is often contradictory.
For example, pick 100 people at random from a nursing home, and try to guess who will live the longest. Sometimes, healthier people will die younger for reasons that have nothing to do with health or wellness - many people die within 2 years of their spouse for example.
If you have seen What Dreams May Come, the character played by Robin Williams and his wife try to deal with the death of their children.
The husband accepts it and moves on, but his wife does not and eventually kills herself. When the husband finds his wife in the afterlife, she is mired in a hellish place from which she cannot escape because she lacks the will to recognize that she is only there by her own choice. It is only when the husband decides he would rather be in hell with her than be anywhere else that she is able to escape.
In Harry Potter and the Sorcerer's Stone:
Dumbledore hides the stone in the Mirror of Erised so that only someone who wishes to find it but not use it can retrieve it.
So the Reverend Mother is saying something along the lines that the first step in the path to becoming the Kwisatz Haderach is to accept that you are not him and may never be him.
This is similar to what happens in The Matrix with Neo. The Oracle tells him that he is not The One, allowing him to just be himself, without the pressure of living up to everyone's expectations, and thus growing into The One without realizing that it was happening.