A - Thanks for the question. It is understandable that you are somewhat disturbed by this practice. It isn't something that our modern society understands very well, so some history, before my opinion, might help.
We are body and soul. Not souls trapped in bodies. This is very important, because it is a vital part of Catholic theology and anthropology. We understand our humanity as being incomplete without a body, which is why at the final judgment our souls and glorified bodies will be reunited for eternity.
In the early Church, there were several heresies that denied the sacredness of the body, including gnosticism. They believed that the body was a mere instrument and ultimately evil. Salvation would come from being pure spirit. There are still elements both within, and especially outside of, the Church that still lean toward this gnosticism.
During these early days of the Church, esp. in Rome, Christians were persecuted mightily by both the government and the Jewish community. They had to start meeting in the crypts of the dead, the catacombs, in secret. They did so because it was illegal for them to gather in public. They started to celebrate the Sacred Liturgy, Mass, within the catacombs - on the tombs of the martyrs. It soon became a common practice to start to hold on to an article of clothing or piece of a saint's body as a reminder of their holiness - which was bodily as well as spiritual, grace enters into us via the physical (think Sacramental theology).
But, this isn't just a Catholic thing. It comes from the Jews, as we see in the Old Testament:
And Joseph made the sons of Israel swear an oath and said, "God will surely come to your aid, and then you must carry my bones up from this place." - Genesis 50:25In Ezekiel 37 we see the "dry bones" becoming enfleshed again, through God's grace. Then in the New Testament we see the accounts of the Evangelists in detailing the care with which the followers of Christ took with his body.
Later Polycarp, an early Christian wrote the following to the Smyrnaeans in A.D. 156:
"We took up his bones, which are more valuable than precious stones and finer than refined gold, and laid them in a suitable place, where the Lord will permit us to gather ourselves together, as we are able, in gladness and joy and to celebrate the birthday of his martyrdom."So, now we have a modern-day Saint being exhumed for his body to be examined. Is it strange to our modern sensibilities, certainly. But, is there something wrong with it? No. Padre Pio's soul is certainly already "in peace" in heaven, his body is waiting to be joined with it. But, until that day comes there is nothing wrong with Catholics venerating it. In fact, it is completely Biblical, Historical and Christian.
The official reason is to:
“respond to certain historic responsibility to guarantee a prolonged preservation of saint’s bodies, using appropriate methods, in order to allow future generations to also have the chance to venerate and care for these relics.”The Catechism ties the Sacramental economy to the veneration of Saints' relics:
Besides sacramental liturgy and sacramentals, catechesis must take into account the forms of piety and popular devotions among the faithful. The religious sense of the Christian people has always found expression in various forms of piety surrounding the Church's sacramental life, such as the veneration of relics, visits to sanctuaries, pilgrimages, processions, the stations of the cross, religious dances, the rosary, medals, etc. (CCC 1674)