Why, in this novel, do some questions end with question marks while other questions end with periods? Is there any logic involved?
McCarthy omits conventions (commas, quotations, and sometimes question marks) because they intrude on the poetry and prose. He's a poet novelist, and he's got a lot of e.e. cummings in him. He wants to expose the words in their bare beauty.
In terms of discourse, Cormac McCarthy uses a lot of polysyndeton, the repetition of conjunctions in close succession for rhetorical effect. He prefaces a lot of his would-be questions with "and" or "but," turning them from questions into statements. Usually, these would-be questions are at the end of a back-and-forth discussion and are used usually by the boy for clarification. Most of the time the father simply says, "yes" to agree. Here's an example (the boy begins with a question):
Why do they have to do that?
I dont know.
Are they going to eat them?
I dont know.
They're going to eat them, arent they?
And we couldnt help them because then they'd eat us too.
And that's why we couldnt help them.
Notice how the boy begins questioning, and then he catches on and turns his questions into statements. The father still answers them as if they were questions.
Here's another example:
Even if we were starving?
We're starving now.
You said we werent.
I said we werent dying.
I didnt say we werent starving.
But we wouldnt.
No. We wouldnt.
No matter what.
No. No matter what.
Because we're the good guys.
Again, the boy asks a line of questioning that begins with questions and ends with statements. The father continues to answer them as if they were questions. Here, McCarthy does not use polysndeton. Instead, he simply wants to show that the boy wants to validate himself in front of his father. Instead of always questioning his father, the boy is showing his father that he can arrive at his own conclusions in the form of statements. In a sense, he affirms what he already knows (that they wouldn't resort to cannibalism; that they're the good guys), and he says these statements also to make sure his father continues to believe them (possibly out of fear that he might be so hungry and weak that he might resort to cannibalism).
Since they only have each other to talk, the two resort to this Socratic method of dialogue. The boys asks, and the father answers. Toward the end, the boy arrives at a conclusion, and the father answers. The boy is the student, and the father a teacher. The Road, then, is a kind of mobile Socratic seminar, a walking discourse.