I am going out on a limb here with this one. This is purely based on my own thoughts and not on any scholarly learning or specific theological knowledge. So please take this with a grain of salt.
When Christ rose from the dead, he appeared, ate, and drank with the disciples in his resurrected body. Catholics believe that his and our resurrected bodies are flesh and blood but they are glorified bodies, meaning they are incorruptible and free of suffering and pain. So why did Christ's resurrected body still have the scars from his Crucifixion? Why was Thomas able to place his finger in the holes in his hands, and his hand in the wound in his side? Why wasn't he "made perfect" without any remnant of his suffering?
Here is my very off the cuff answer: In Christ's suffering, he was glorified. In his perfect sacrifice, his perfect laying down of life out of love for us, his perfect uniting of his will to the Father's, he was glorified through the Father. In other words, his wounds are a physical reminder of his greatness. God himself died for us, and in that action he is given all the glory. Christ was made perfect through his suffering (Hebrews 2:10), through his great sacrifice. His resurrected and glorified body is as perfect as it can get.
One might ask herself to remember the moment of highest glory in her life, the moment where she felt she achieved true greatness. I suppose some might remember winning some meaningful award or being recognized for some long-toiled over achievement. But I think many would remember the moments when they performed a significant sacrifice for the good of someone else. Perhaps it is when a women labors to give birth to a child, or when someone helps a homeless man to find work, when someone gets a heartfelt thank you from a needy person after working long hours in a soup kitchen, when a sidewalk counselor rescues a woman and her baby from abortion and sees that they have the resources they need, or when parents watch their children get married and know their long years of teaching have paid off. These moments of greatness, these moments of glory, are what they are because of the loving sacrifice it took to get there and the powerful result it achieved. And the signs of that sacrifice, the wounds, the scars, the memories of hard work, make that glory all the more powerful. Being born into a certain bloodline doesn't grant true glory; sacrifice does.
Now, of course, Christ is perfect and glorious simply because he is God, the Creator of all. But he shows us his glory in the powerful message of the Cross, in his laying down of his life for us. The wounds in his hands and side are signs of his great Love. Christ's glorified body is his Crucified body, Resurrected. The marks of that body are altogether glorious.