Pencil or Ink on Paper that is clear it's just that and not some scanned and then "digitally inked" work, you usually can tell because of the coloring of the paper, the coloring of the strokes and pretty much the general "non 100% clean" nature it has.
Digital Work, even the one that is made using traditional lines as a baseline, will look extremely clean and without the slight imperfections a "clean and inked" traditional work would have.