The thing about thunderstrike is, used en masse, it can defeat ridiculous amounts of units as long as they aren't immune. Nine e9 tuatha sorceresses, for example, should kill about 27 units per turn, even before accounting for the splash damage (which also causes fatigue, which can allow your normal troops to defeat them more easily and even cause them to pass out altogether) which should allow them to kill significantly more. And because they have e9 in this example, the extra reinvigoration will help them to keep throwing off these thunderstrikes. Aim is not critical, per say, but it does help make each thunderstrike more efficient. Thunderstrike is also more efficient under storms, when you cast summon stormpower. Which can then allow your a2 recruitables to also spam thunderstrike. So a nation like TNN can mass a lot of thunderstrikers if it needs some chaff clearing. Of course, at 6 evo, you get wrathful skies... which will eventually kill any army that's not completely immune to lightning, and would not be hard for just one mage to cast behind a handful of lightning immune thugs.
Here are a few spells to try if you still find magic too inefficient: curse of the desert, stellar cascades, strength of giants, legions of steel, flaming arrows, wailing winds.
Curse and stellar cascades can weaken troops enormously, and even outright kill them with enough casters, but only require a few to have a pretty significant effect on tough troops. Strength of giants through flaming arrows are good army strength multipliers, and will make your own troops even more effective on a unit per unit basis. Wailing winds, well, used appropriately it will let you rout armies with much fewer casualties, which will have the side effect of giving you lots of easy kills in battles.
Also I agree with thejeff with regards to banelord kitting, but if you're using them with skellyspam as I've suggested you can drop the air boots and horror helm, and they'll still work. Banelords are NOT as durable as they might seem though, and should not try to take on large armies by themselves. They work better as raiders and army support. Taking on 100+ man armies single-handedly is the domain of real SCs and upper end thugs like sidhe :P And a final note on thugging: one of the biggest killers of thugs vs conventional armies is fatigue. Having more than a net +1 or 2 fatigue per turn is pretty much suicide.
Edit: Oh yes, I forgot. I was going to say that I once won a game against full on impossible AIs using unequipped sidhe lords as though they were troops
I won the significant majority of my battles with those, and only started using real thugs in the end because it was taking too long to finish the enemy off. I lost probably less than 10 sidhe lords that game.