Sir John Vaughan [can't find any evidence for the "Owen" either, but that is another issue...], like many other people in Ireland at that time, did not leave a huge trace, but still, there are quite a few contemporary records, deeds and charters. None that I can find name his wife. There is a Victorian suggestion that his wife was a Barbara Sydney, but no evidence [apart from the fact that his daughters are Sydney & Barbara...].
The only source of the name of his wife being Barbara Herbert appear to be family trees. Most stop there, but Geni has her as a daughter of Richard Herbert, Lord Cherbury & his wife Magdalen Newport [who married in 1581] Apart from the lack of evidence, there is also the impossibility of ages; Richard Herbert would be 8 & Magdalen 4 when this Dorothy was said to be born in 1565 [although who knows what dates she should have as she seems to be ficticious...].
As his wife seems to be both unknown & at this stage, unknowable [unless some new doculments come to light], there doesn't seem to be any justification for keeping Dorothy Herbert as his wife. Unless there is a Welsh source?
My connection is through Sidney Vaughan, daughter of Sir John Vaughan.
What do you think Erica Howton?