Permanence: it depends which ink you use. Only pigmented ink is permanent. Dye ink is fugitive (it fades). Graphite (pencil lead) is actually extremely permanent. We have pencil drawings dating back from Da Vinci and way before him.
Why pencil: first, pencil is used on the mat of a matted print, or on prints made on rag paper. Ink (pigmented) is used on glossy prints since pencil won't adhere to glossy surfaces. Personally, I think pencil is more aesthetically pleasing --more natural if you will-- than ink on rag paper. Also, ink has a tendency to soak into rag paper and make a mess.
Since pencil is just as archival as pigmented ink, it esentially boils down to a matter of taste. I prefer pencil for rag paper and mat board and ink for glossy papers.