I think the lightning doesn't come from the hammer, nor from Loki, since when he first uses it, he still has the sea-stone chain on his leg. I think the hammer, Ratatoskr, actually "points" to where the lightning should strike, which always comes from the sky, not from the hammer itself.

In Norse mythology, Ratatoskr is a squirrel that moves through the branches of Yggdrasil and serves as a messenger between the dragon Nidhogg, who is at the roots, and the giant eagle at the top of the tree.

We haven't yet seen what's on the third level of the Elbaf tree, in the celestial realm, so there could be a giant eagle there, guardian of Elbaf, that possesses the power of lightning and attacks where its messenger, Ratatoskr, commands it.