Herodotus isn't capitalizing God, your translator is. Greek had no lowercase letters when Herodotus was writing and most of our medieval copies don't use capitals at all. Greek doesn't need to specify what god a speaker is talking about when ὁ θεὁς is used. Also, depending on how old your translation is the oblique cases of Ζεύς (i.e. Διός, etc.) may be getting translated as "God," I've seen it done in some old translations before

To add to what's already been said, I've seen it suggested (I can dig out the reference if needed) that when Herodotus uses general terms like this he is talking in the same way that "ordinary" ancient Greeks would have done when attempting to explain the inexplicable. In a culture with hundreds of different deities, a lot of the time you wouldn't know which one of them was responsible for a certain phenomenon, so you'd attribute it to ὁ θεὁς, "the god", οἱ θεοί, "the gods", or τό θεῖον, "the divine" (Herodotus uses this one a lot, too). There are other times when the identity of the god in question may be inferred from the context. So if Herodotus is talking about something fulfilling an oracle, "the god" will probably be Apollo; if he talks about "the god" striking someone with his thunderbolt, he probably means Zeus.

There is a ton of literature on Herodotus, but a good starting place is John Gould's little book Herodotus (1989). On the religious aspect in particular, see Thomas Harrison's Divinity and History: The Religion of Herodotus (2002) - chapter 6 may be of interest as this deals with the terminology of the divine. There are also a few companion volumes - collections of essays by different authors dealing with different themes - Brill's Companion to Herodotus (2002) and The Cambridge Companion to Herodotus (2006), the latter being more accessible.