Apparently the Welsh first name Daffyd doesn't exist - there is a Dafydd, but Dafydd is apparently very unlikely to drift linguistically across to Daffyd because the Welsh alphabet makes Daffyd and Dafydd sound completely different. Is the use of Daffyd in H:RW possibly a typo?
Dafydd is the normal and most commonly seen version (as in Dafydd ap Llywelyn in the 13th Centurey or Dafydd James in Rugby) but Daffyd also exists, in real life but also more famously in fiction (e.g. Daffyd Thomas - the only one in the village)
It was also commented on that Ap Brendan is a very odd surname, because it means "son of Brendan", and Brendan isn't a Welsh name, but using the "Ap" convention is an unusual choice even today, and Ap Brendan is apparently the equivalent of "de Johnson" - it sounds rather weird. Given that Brendan is an Irish name but Dafydd is a Welsh name, is the use of the two meant to indicate that Gwynedd was a melange of Welsh/Irish descendants or enthusiasts, despite the Welsh name of the planet?
Indeed, ap xxx is rather archaic and is similar to the xxx-son in scandinavia, or ibn xxx in arabic, stating a family line by naming a parent (of course, Arabic has the opposite to in abu - father of). It's a bit different to "de xxx" or "von xxx" in German as both are more more "of xxx" (relating to a place or family rather than a specific relative).
Brendan we can argue over ;) Yes, it's of Irish origin, but there are people in Wales with that name so it's not impossible for it to exist on a "welsh" world. And don't get me started on variant forms of Irish names :P
My thought is pretty much as Herb says - a few centuries of linguistic/cultural drift (and some typos on birth records) and a general mixing of cultures mean modern rules don't necessarily apply, not to mention that while the world and it's leader have Welsh names (quite possibly effected - who knows if he's using that form of name to appease a 26th century version of Meibion Glyndwr). Or, as you say, it could be the 26th century attempt to create a "welsh" culture, in the end just as authentic as the Franco-British trappings of New Avalon.
In the end, its fun to speculate as to why details of the setting are they way they are.