Haven't had time to read through all the replies on this (just most), so excuse me if I repeat anything previously stated.
As far as I remember Kildare was one of the last refuges of the 'Jacobite Free and Accepted Masons' as opposed to the 'Hannoverian Freemasons' of the Grand Lodge of England (ie todays Freemasons) and their local clones. The history follows general history, Jacobites big in Ireland and Scotland after they get the boot in England. But over time, the failure of Jacobite uprisings and the insidious infiltration into Scotland and Ireland of either out right Hannoverian factions, or at least 'moderate non-Jacobite Catholics' who'd done a peace deal with them, saw the old school 'Jacobites' (more of a culture of 'aristocratic libertinism' by then rather than a political stance) get pushed into the fringes. I think one of those fringes was Kildare etc. The original Masonry (said to be related to Templarism) was Jacobite and moved were they went. In fact it seems to have evolved with Jacobitism. The Hannoverian stuff was just the 'commercial version' :) and wasn't the real 'grassroots' thing. The two also used slightly different symbolism or rather gave different emphasis to traditional symbols. Hannoverian Masons certainly used the skull and cross bones in the 3rd degree Master Masons Ritual (a death rebirth deal) but didn't really emphasise it much else where (maybe as they were 'respectable bourgeoisie'). Whereas Jacobite Masons seemed to love it (maybe because they were a 'rebel faction').
Its also possible there was a Templar inheritance, that was lost on the Hannoverians. Most theories of Templar > Mason evolution are absolute rubbish. However any genealogical research shows the same families were often involved in both (including my ancestors, which is how I found out. And no I haven't preserved a secret family tradition, or have I? {insert spooky organ music} ) But anyway, in King John's time, the Master of the Knights Templar in England was one John St Leger (descendent of a Burgundian arriving with William I in 1066). In the 17th century a senior Jacobite Mason in Ireland was his direct descendent, also called St Leger (and yes he was a gambler and he did found the famous horserace of that name). His faction disappeared off to the countriside after the 'English' took over Dublin! :)
Now the Templars did use the Skull and Crossbones symbol without any doubt, it can be checked in any archeological study. It came from the Lady of Sidon story I think, where a dead woman gives birth to a skull between her thighs bones in a grave after having sex with a Crusader. Weird medieval necrophillic legend with alleged esoteric meaning (don't ask me what)! But lots of Crusaders used the symbol after this, most noticably many Templars. The Templars were also said to have kept a skull as a secret relic, possibly the infamous 'Head of Baphomet'.
Other people used the Skull and Crossbones of course, so its not just Templar or Masonic automatically. These others included some Pirates, not all though, some used crossed swords and a skull or just crossed swords, and many used something completely different, a hawk for instance or a simple plain black flag. The flag was the symbol of the captain of the ship and his personal totem, so none were exactly the same. Curiously those who first used different versions of the Skull and Crossbones as a symbol seem to have been often of Irish or Cornish descent (as far as my limited research here indicates) and were originally privateers rather than pirates (state sponsored pirates who fought national enemies, before going rogue, a bit like bin Laden). These people were often 'libertine aristocrats' like the last Jacobites became, so its tempting to surmise a link. Though as yet I've not come across one. It would make sense for ex Jacobites to become Privateers and Pirates as many certainly became Mercenaries in later years (including St Legers). So these graves MIGHT be very interesting.
Steve