No idea but as the town was on Holy Island, might it be that the Welsh lived there (in the town) but the English were just passing through?
Head as in headland at the end of the island. There is a Holy Head in Cornwall too, but that one is translated into Cornish (related to Welsh) as Pensans. I.e., Penzance.
Lots of place names aren't directly translated. The Welsh have names for some English towns and cities, too, though I'm not sure how often they actually use those names.
I've always wondered; why do we pronounce it 'Holly-head' in English instead of 'Holy-head', especially given that it is Holy Island?
Is it the same/similar reason we pronounce Holyrood in Edinburgh the same way?
There's nothing much there aside from a ferry-port to Dublin. It's Welsh name, Caergybi is named after Saint Cybi's monastery, which itself was originally a Roman fort (hence the name). The Latin name for the fort is unknown but it became Caer Cybi in Welsh. The town of Holyhead/Caergybi grew around it. The English name refers to the "head of Holy Island" and the Welsh name refers to Saint Cybi's fort.
When the two words Caer and Cybi are joined the second word undergoes Soft Mutation (c to g) and so becomes Caergybi.
funny that the welsh pronunciation sounds like the danish "kirkeby" (churchtown)