The short answer is that John has long been one of the most common male forenames, and that Wales was conquered by the English before fixed surnames were used. To elaborate and explain: Most Welsh surnames are based on a patronymic system - Welsh people were traditionally named things like Owain ap Siôn - Owen son of John.The letter J made its way from England to Wales via English aristocrats, administrators and other immigrants, and so did the system of fixed surnames. Owain would be given a surname based on his existing name; if he’d been English he might have been called Johnson, but in Wales Jones or Siôn or John might have been used instead. His children would now use this surname too, instead of being called ap Owain.

As Welsh-speakers became increasingly familiar with English over time, and with the letter J, they have tended more and more to use forms of names that have a J in rather than the versions where J has been changed to the closest native equivalent, Si. The administrators of church and state were servants of the English monarch, and generally kept their records in English, so someone might be recorded as David Jenkins in a parish register but have been called Dafydd Siencyn by his Welsh-speaking neighbours.

I’ve seen monumental inscriptions where the English form of the name is recorded with the date of death, and the Welsh form of the forename is given in a poem following. As ordinary people became literate, it became possible for names to be spelled consistently over time in records - before people could read, they told the vicar, who was often not a local man, their name and he wrote it how he thought it should be spelled, and that spelling might be differently from how the previous vicar had spelled it. Once people could correct the vicar because they knew how they spelled their name, they could in theory ensure it was spelled the same every time and that their children spelled it the same way they did. But because English was the language of power & authority & official records, of education and worldly success, the consistent spelling that ended up being used in most Welsh names in Victorian and Edwardian times was the English spelling and not the Welsh ones. There has been a gradual regrowth of Welsh-language names (as opposed to Anglicized Welsh names) over the last few generations.