WHICH Variables have the unwanted "Don't Know" or "Refused" categories?
What your analysis variable does is segregate observations, it does not remove any values of "Don't Know" or "Refused".
From the documentation for the DOMAIN statement for Surveylogistic: (emphasis added). So you get an analysis of the subpopulation where analysis = 1 and all of the observations.
The DOMAIN statement requests analysis for domains (subpopulations) in addition to analysis for the entire study population.
Typically you set the variables to MISSING, which means the observations will be excluded from the model OR recode them to another category you do want to include.
Setting to missing would be something like
If var in (7, 9) then call missing(var);