That's not good. A total disappearance over night with no signs of stress is pretty crazy. Makes me think something ate it. Have you had anything else disappear like this? I'm thinking the dreaded bobbit worm (not sure if they eat clams though)
Could it have died in the evening and been "cleaned up" by scavengers (hermit crabs, nassarius snails, sea stars...)?
Have you looked to see if there is a hole bored through the shell? I've seen photos of Tridacna shells where clams have been killed this way. Can't remember if it is a worm, sea star or snail that does this.
I think I'd be staying up late tonight to try to determine if there is something that ate it.