There's one just down the road from here in Upper Weardale.
"They just symbolise death."
That seems to me the most elegant explanation, because it explains why both these graves and pirate ships (which would BE death to their victims) show this symbol. But it leaves me with niggling doubts: why would some graves get them and not others? Was it just a matter of the family's taste?
I must admit I'm very dubious about the Templar/Mason thing, although I must also admit my relative ignorance on those subjects. Is there actually any solid evidence at all to suggest that the skull and crossbones is a symbol used by either Templars or Masons? It would have to be a pretty popular symbol amongst these people for us to jump to the conclusion that these are Masonic/Templar graves, because there's also a great deal of evidence to suggest that it's a symbol of pirates, for a start (not that I'm suggesting these are pirate graves, jim lad).
Ocifant: the plague thing had crossed my mind, too, but surely there'd be more of 'em about if that was the case. There's only the one in the churchyard I know, and I'm damn sure more than one person died of plague in that village (which is called Saint John's Chapel, by the way, and which John Wesley described as "the most godless place on earth").