What does "to have something to them" mean?

Solution 1:

OP has misparsed the usages. You can have something on someone (you know something "secret" about them, giving you power to "blackmail" them). But you can't have something to [a person].

The cited usages are versions of the idiomatic there's something to it, meaning it's not a completely daft idea - there's at least a grain of truth in it. Or perhaps there is some point in doing it.

EDIT: In the same general area, it's worth noting there's nothing to it, which usually means it's easy. It is sometimes used to mean the exact opposite of the usage under consideration here, but I think most people use there's nothing in it when they mean it contains nothing of value or truth, though it can also mean there's no difference [between two things being compared].

Solution 2:

He means that the "incantations" had some content, some meaning, some "substance", because they seem to have had some effect.

That is, the events (seemingly) lend credence to the belief that these "incantations" (or in the case of Hendrick Hertzberg, "theories") were not empty and meaningless.

Solution 3:

He means that the "incantations" had some content, some meaning, some "substance", because they seem to have had some effect.

That is, the events lend credence to the belief that these "incantations" (or in the case of Hendrick Hertzberg, "theories") were not empty and meaningless.

Oh-- and as for your question title, "them" does not refer to anyone; it refers to the incantations and theories, respectively. I would have edited your title to "..something to IT", but perhaps that was the crux of your confusion.