"It seems to me that the lightning strike has a much reduced chance of hitting."

It does.

I think your ability to hit with lightning strike has nothing to do with your attributes beyond what they do normally with your ability to hit. Because the skill is specifically tied to the class I wouldn't be at all surprised if class level is A, if not THE, factor.

I had He'li killed in one of my games, bit annoying had to go a long way back to my lasted saved games!!
As I went past her bar, the bandits (or whatever) in the upstair bit tried to come down and fight me, but got her instead.