Mhh, in the case of Brave Shields, I mention this scriptlet in the README:

window.addEventListener('DOMContentLoaded', () => {
    function mutenuke() {
        document
            .querySelectorAll('div[class*="comment_collapsed"]')
            .forEach(node => {
                if (node.textContent.startsWith('reply from someone you muted')) {
                    node.style = 'display: none';
                }
            }
        )
    }

    // Run on initial page load
    mutenuke();

    // Watch for dynamically loaded content
    const observer = new MutationObserver(mutenuke);
    observer.observe(document.body, { childList: true, subtree: true });
})

My userscript does not include the event listener. IIRC, the extension executes userscripts after the DOM has finished loading, so the listener shouldn't be needed. So I think this shouldn't be the issue, but I could of course be wrong.

Btw, since I realized we don't need API keys anymore with nsec authentication, I could, in theory, start writing a TUI as an alternative client, haha. Could be fun?

Edit: Oh, maybe you meant runAfterHydration(mutenuke)