Let's clear this up once and for all.

"It" is insulting.

To refer to a human being as "it" is to demean them, to label them as "less than human". Racists use "it" when the want to ultimately dehumanize their victims. Even in fictional or mythological settings non-human intelligent beings are always referred to as "him" or "her" even when gender is unclear or irrelevant.

Applied to God this is even worse.

"It" is still singular, so it doesn't get round the singular/plural problem. Calling God "it" would still imply that he is singular in the exact same way that "he" does.

So in short 1. No grammatical benefit 2. Very insulting.

That's why it isn't done.