I think you'll find the shrink wrap will obscure your compass/clino eyepiece and make instrument reading more difficult. Even though it's "clear" when wrapped directly onto a surface, if several layers of it are stretched across the eyepiece they may act like an unfocused lens.
Several years ago I applied a bead of silicone around the edge of the compass and clino discs. Like rchrds said, they are press-fit into the housings and therefore not totally sealed. The silicone helped - at least for a while. I peeled it off eventually, mainly because I haven't surveyed in many nasty, wet, muddy caves in recent years.