Question

1. Is it too late to call him.

(What does 'it' refer to in the sentence? Weather?)

Answer 1

"It" refers to the situation or "the way things are". "It" wouldn't be the weather, because you don't measure weather with time adjectives (such as early or late).

You might be thinking about inviting him to a meeting, for example, when there is not enough time for him to get there.