If Covenant is indeed set hundreds of years after David attacked the engineers, then Shaw is probably dead or was left in an engineer cryo-pod. Judging by that nap the engineer in Prometheus took, I'd say it's entirely plausible. But I wonder if the effects of such a long sleep would effect humans differently than the engineers. Ripley pulled a long stretch, but not hundreds of years. Could brain death or insanity occur after say, 100 -150 years? Either way, David definitely appears to be hostile towards humanity, whether this extended to Shaw or not is the thing. I Personally don't think it's set that far into the future from Prometheus, but you never know.