There are a couple of things I can think of:

1. You might not have chosen the correct race to gain that ability. Check in the unit details screen or the unit design screen to see if your units have Amarian Blood (which grants the lightning attack) or if they have something else.

2. It might possibly have been removed from the action bar. In that case, you should be able to find it by opening the 'Spells' or perhaps the 'Skills' list (click the button labelled 'Spells' or 'Skills' under the action bar in a tactical battle). If it's there, you should be able to bring it back into the action bar by clicking on the circle with a star in the middle, and then clicking a spot on the action bar, or you can use it from the pop-up menu from the button.

3. If you created a custom faction of a non-Amarian race, played for a while and created a few custom units for it, and then created a new custom faction with the Amarian race but used the same name, there at least used to be a bug where your custom units from the previous version of the faction and would use the old version's race instead of the new one.

Not without modding. This is a bonus for Amarian blood, and should show up at no cost on any units with that blood trait.

No, everything was the same with this ruler, as with the one I had the last few times whose spearmen could shoot lightning bolts. In fact, starting up a new game with that old ruler also gave me spearmen who no longer could cast lightning bolts. So something appears to have changed in the game, itself.

Same Parirden-like ruler I've used before who had no problems in earlier versions. Same Amarian blood. Happens while using a mod, and while using none. This is happening with a new game, so it's not a case of problems inherited from differences between new and old code.

EDIT: Mana! Should have realized. I missed the most obvious thing of all: each soul cast requires mana for use. The number's gone up (it's 15 per cast, now), I think, and so my nascent team couldn't raise a single blast. Bah.

Thanks for the assistance, regardless!

SON OF EDIT: Casting cost has gone greatly up. Enough, frankly, to make the ability to just about useless, unless you have mana coming out of your ruler's ass. In which case, you might want to put a few tech buildings on him/her to harness it better.

menh.. the lightning attack is rarely if ever worth the mana now.

definitely when compared to any normal spell at about the same mana cost.

One caveat is when there is a Banshee to fight.  This faction trait means you don't have to make custom units to deal with them.