Hi lindydonna,
The main difference between silk thread and wire is that silk is highly absorbent while wire is not. Dirt accumulated in the drill holes due to the use of wire will result in quality pearls losing their luster. This problem is greatly reduced when quality pearls are strung on silk thread. When the thread becomes dirty or if spaces between the pearl and knot occur, it is time to restring the necklace.
As Russ Nobbs had mentioned, knotted necklace should be restrung depending on how often the wearer wears it.
There are a variety of materials to knot pearls. Pure silk could be used if you are stringing high quality pearls. Pearl silk is also available now, being a blend of pure silk and polyester thread. For mineral and imitation pearls, you could use polyester thread, nylon thread or a mix of both these materials, called "stringth" thread.
Also, a fully knotted pearl necklace has the advantage of not spilling the pearls everywhere should it snap; only one pearl would slip out if that were the case.
I hope this information is useful to you! All the best in your stringing endeavors.