There's a difference between "children" and "the children". We're not talking about specific children, but children in general.
The rule isn't that the verb should literally be the second word, but that the verb comes in the second position. 'Welche Fragen' occupies the first position as a single unit. It's akin to when you see 'Die Kinder spielen'; the verb is the third word, but it is in the second position.
So what is it in this sentence structure that actually indicates what is the subject and object of 'have'? It looks like it should read which questions have children, ie the questions are the owner. I realize that is nonsensical in context but there seems nothing in the sentence structure that stops this interpretation? I would want to structure he original german sentence as 'children have what questions?'