To the Imperium's knowledge, the Necrons don't name their ships. Confirmed sightings do assign tagnames to energy signatures, though, for Ordo Xenos records (much like they assign names to all alien vessels, since even their real names wouldn't translate well into High Gothic). Since Necrons don't have very much personality, you could try to name them creatively or just assign them numbers ("Deep Space Anomaly 1234.567") or something like that.