Page Query in wrapPageElement of Gatsby?

I'm trying to use dynamic query in my wrapPageElement.

That will never work. wrapPageElement is a shared API between gatsby-browser.js and gatsby-ssr.js that wraps component across pages, it's not intended to trigger queries, it doesn't make sense because page queries happens in pages (or templates) and that context is missing in the wrapPageElement.

The idea is that, there is a Nav element, which is part of the main Layout, so it should be able to list my pages.

You can use a useStaticQuery to display all pages like you are doing in the query above, but you don't need to filter it at all. Static queries don't accept dynamic values, like $locale is (hence the name) so any kind of filtering would need to be applied in JavaScript code directly.

It's quite common to use isolated components, something like:

import { useStaticQuery, graphql } from "gatsby";

export const useNavQuery = () => {
  const { pages } = useStaticQuery(
    graphql`
      query PageLayout {
        pages: allMarkdownRemark(
          sort: { fields: [frontmatter___title], order: DESC }
          filter: {
            frontmatter: { draft: { nin: true } }
            collection: { in: ["pages"] }
          }
        ) {
          nodes {
            frontmatter {
              title
            }
            fields {
              slug
            }
          }
        }
      }
    `
  );
  return pages;
};

Then:

import React from "react"
import { useNavQuery } from "../hooks/use-site-nav"

export default function Nav() {
  const pages = useNavQuery ()
  return <h1>/* your loop through pages */</h1>
}