Q: Since Saber and Gilgamesh have physical bodies in Fate/Stay Night, can Shiki see lines on them? (@LestatDusk)

A: Not just when they have a physical body, the Mystic Eyes of Death Perception are effective even when they're in spiritual bodies. For Shiki [Ryougi], if the opponent can be recognized as "living" (not "life", but "live"), she can see the lines of death. For example, the ghosts in Overlooking View were dead, but they were "living" in the sense that they can interfere with the current world.
Also, why she didn't succeed against the Sarira in Araya's arm is because it belonged to an enlightened one who achieved "becoming extinguished, alive." To kill it by the lines of death means she has to decipher advanced "lines of death" levels higher than the normal concept of death. But what's sad about bones is that rather than having to do that, they'll turn into ash if you burn them. If you have time to be using Death spells, level up and beat it physically.

TYPE-MOON Fes. Official Pamphlet 10th Anniversary Q & A Booklet