The original question, which was a good one, seems to have gotten sidetracked by a specific necklace. In my humble opinion, the answer like many others when dealing with collectibles is: "IT DEPENDS".

Many of the worlds great museums think nothing of restoring ancient material either by cleaning or repairing or whatever. I have always leaned towards not touching anything, sometimes I won't even wash the dirt off. There are case though when a bead or group of beads are in such poor condition, that leaving them alone may be a disservice.

Some of the marble beads for example are so badly beat up that they almost deserve being restored. Drilling something that was never intended to be a bead originally, well that is doubtful in my mind. There are also cases with ancient beads where the burial patina is so heavy one cannot see the original bead.

In the end of course you own the bead and can do whatever you want with it, though hopefully not modifications meaning to deceive someone as to what it was originally. I would like to hear more comments on the original question.

Below is a bead that started life as an ancient eye bead and had a more modern face cane attached, obviously intended to deceive a potential buyer.