To me, the sentence implies that he should have already been up.

Actually it is bizarrely the opposite. Rather than indicating "surprise" that her husband is already up it in fact indicates a belief that the husband "ought to have been" up already. For example, "are you ready yet" would be used if you thought someone was taking too long and wanted to hurry them up. The implication is that you expected them to be ready some time ago and you are surprised they are not.