Bit of a breakthrough on the local research front! At the time, the nearby village of Minsterley did not have its own church so weddings, burials etc took place at Westbury (3 or 4 miles to the west).The register there contains the following entry:

1st March 1683 Anne Nicholas murdered (truculenter occisa) - burial

The latin phrase means something like 'savage death'. 1683 was the year before the ballad first appeared, so this is almost certainly the lady in question. There are a number of baptism entries which could refer to Anne and her murderer (Francis Cooper), the most likely of which would indicate that he was aged 27 at the time and she 23.

Most fascinating of all, however, is the following entry:

24th March 1683 Ichabod son of Fancis Cooper, homicide, and Anne - baptism.

I'm still trying to think through the implications of this but presumably it means that either Anne had already given birth before she was murdered (as opposed to being pregnant) or that the 'Hogstow One' had also fathered a child by another woman - also called Anne - before he was hung for his crime. Interestingly, the ballad collected by Pepys does refer (verse 8) to him having kept company with "another maid beside" so who knows. I think what I can at least confirm is that ballad was based on an actual historical event. If I find out any more I'll keep you all informed.