Yes, both my clients are NY nonresidents.  I am using ProSeries.  As I recall, I did the federal MFJ, then opened a NY nonresident return and sorted out the income between NY and non-NY source.  At some point the software must have noticed that only the husband had NY source income, so it made the filing status MFS for him and ignored the wife.  No effort on my part, I had to do some research to make sure it was the correct way to file.