Orly? I just started up a new patch and looked at them. They're all holy, and Lightning Stab/Hallowed bolt also has lightning. I also imported a freshly patched version of FFT:C and found the same thing.
Well, FFT 1.3 or whatever patch might have changed it, but in the original, the holy swordskills were bugged and didn't actually have the elemental properties that the description said that they did. They simply took on elemental property of whatever weapon they had equipped. The computer however is not aware of this which is why they will not attack you with holy swordskills if have a holy immunity, like if you were wearing a chameleon robe.