Having both Lightning damage and Thunder damage is going to be problematic, I am certain...
Thunder damage is obviously the new Sonic damage, but it is a bad name for the old concept. The idea of thunder is inseparable from lightning and electricity. It would be just strange to use a Thunder attack that attacks with sound, if there is no lightning involved at any point.
I think Sonic/Thunder is a damage type that can probably be removed from the game without problem. I really don't know why it is even in the game to begin with. The idea of a pure concussive sound wave is not really that different than normal physical damage. I would much rather have a pure Wind, Water, or Earth types (perhaps an Asphyxiation type), simply because they work well enough in videogames I like. Sonic doesn't even have that going for it.